Summary:
Initial | After 10 cycles | |
---|---|---|
R factor | 0.3783 | 0.3200 |
Rfree | 0.3783 | 0.3383 |
RMSD Bond Length | 0.0212 | 0.0221 |
RMSD Bond Angle | 2.478 | 2.509 |
RMSD Chiral Centre | 0.461 | 0.472 |
Result:
Initial | Final | |
---|---|---|
R factor | 0.3783 | 0.3200 |
R free | 0.3783 | 0.3383 |
Rms BondLength | 0.0212 | 0.0221 |
Rms BondAngle | 2.4783 | 2.5091 |
Rms ChirVolume | 0.4614 | 0.4720 |
Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Rfactor analysis, stats vs cycle |
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############################################################### ############################################################### ############################################################### ### CCP4 6.3: Refmac_5.7.0032 version 5.7.0032 : 05/09/12## ############################################################### User: Administrator Run date: 10/ 5/2013 Run time: 18:43:55 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 Data line--- refi type REST resi MLKF meth CGMAT bref ISOT Data line--- ncyc 10 Data line--- scal type BULK LSSC ANISO EXPE Data line--- solvent YES Data line--- weight AUTO 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 SIGFP=SIGF FREE=FreeR_flag Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM Data line--- tlso addu Data line--- PNAME lizozim Data line--- DNAME 1 Data line--- RSIZE 80 Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: C:/SOLVE_REFINE/lizozim/mr-refine-build\lizozim-xds-p43212.mtz Spacegroup information obtained from library file: Logical Name: SYMINFO Filename: C:\CCP4\6.3\lib\data\syminfo.lib **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r11.pdb Output coordinate file. Logical name - XYZOUT actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r111.pdb Input reflection file. Logical name - HKLIN actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\lizozim-xds-p43212.mtz Output reflection file. Logical name - HKLOUT actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r111.mtz Cell from mtz : 78.713 78.713 36.840 90.000 90.000 90.000 Space group from mtz: number - 96; name - P 43 21 2 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : C:\CCP4\6.3\lib\data\monomers\mon*cif Parameters for new entry and VDW: C:\CCP4\6.3\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 Bulk solvent based on Babinet"s principle 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 0.0268 Refinement of individual isotropic Bfactors Refinement resln : 55.6587 1.3660 Estimated number of reflections : 31789 Free R exclusion - flag equals: 0 Auto weighting. An attempt Refinement cycles : 10 Scaling type : Bulk solvent using using Babinet principle 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: 55.6587 1.3660 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 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 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 :C:/SOLVE_REFINE/lizozim/mr-refine-build\r11.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: C:\CCP4\6.3\lib\data\atomsf.lib
Number of atoms : 917 Number of residues : 129 Number of chains : 1 I am reading library. Please wait. mon_lib.cif WARNING : large distance for conn:TRANS dist = 5.595 ch:AA res: 47 THR --> 48 ASP ideal_dist= 1.329 WARNING : reverse conn, will not be used WARNING : link:SS is found dist = 1.981 ideal_dist= 2.031 ch:AA res: 6 CYS at:SG .->AA res: 127 CYS at:SG . WARNING : link:SS is found dist = 2.020 ideal_dist= 2.031 ch:AA res: 30 CYS at:SG .->AA res: 115 CYS at:SG . WARNING : link:SS is found dist = 2.038 ideal_dist= 2.031 ch:AA res: 64 CYS at:SG .->AA res: 80 CYS at:SG . WARNING : link:SS is found dist = 2.068 ideal_dist= 2.031 ch:AA res: 76 CYS at:SG .->AA res: 94 CYS at:SG . -------------------------------- --- title of input coord file --- PDB_code:2ZIL PDB_name:HYDROLASE PDB_date:18-FEB-08 -------------------------------- ATTENTION: atom:CE MET 12 AA is missing in the structure ATTENTION: atom:CE1 HIS 15 AA is missing in the structure ATTENTION: atom:NE2 HIS 15 AA is missing in the structure ATTENTION: atom:CD2 LEU 17 AA is missing in the structure ATTENTION: atom:CB ASN 19 AA is missing in the structure ATTENTION: atom:CG ASN 19 AA is missing in the structure ATTENTION: atom:OD1 ASN 19 AA is missing in the structure ATTENTION: atom:ND2 ASN 19 AA is missing in the structure ATTENTION: atom:CE1 TYR 23 AA is missing in the structure ATTENTION: atom:CZ TYR 23 AA is missing in the structure ATTENTION: atom:OH TYR 23 AA is missing in the structure ATTENTION: atom:CE2 TYR 23 AA is missing in the structure ATTENTION: atom:CD2 TYR 23 AA is missing in the structure ATTENTION: atom:CG2 VAL 29 AA is missing in the structure ATTENTION: atom:CE1 PHE 34 AA is missing in the structure ATTENTION: atom:CZ PHE 34 AA is missing in the structure ATTENTION: atom:CE2 PHE 34 AA is missing in the structure ATTENTION: atom:CB ASN 37 AA is missing in the structure ATTENTION: atom:CG ASN 37 AA is missing in the structure ATTENTION: atom:OD1 ASN 37 AA is missing in the structure ... and more ... Number of chains : 1 Total number of monomers : 129 Number of atoms : 1969 Number of missing atoms : 76 Number of rebuilt atoms : 844 Number of unknown atoms : 0 Number of deleted atoms : 0 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 Number of distances : 0 Number of angles : 0 Number of torsions : 0 Number of planes : 0 Number of chirals : 0 Number of intervals : 0 -------------------------------------------------------------------------------- --------------------------------------- Standard External All Bonds: 1746 0 1746 Angles: 3104 0 3104 Chirals: 132 0 132 Planes: 302 0 302 Torsions: 706 0 706 --------------------------------------- **** Info from mtz file **** FreeR flag 0 Number of "free" reflections 1280 Number of all reflections 25101 -------------------------------------------------------------------------------- Number of reflections in file 25120 Number of reflections read 25101 CGMAT cycle number = 1 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 56 LEU HG - A 56 LEU CD1 mod.= 61.89 id.= 108.00 dev= 46.108 sig.= 3.000 A 98 ILE HB - A 98 ILE CG1 mod.= 68.15 id.= 109.00 dev= 40.849 sig.= 3.000 A 124 ILE HB - A 124 ILE CG1 mod.= 61.60 id.= 109.00 dev= 47.399 sig.= 3.000 **** Chiral volume outliers **** Chiral volume deviations from the ideal >10.000Sigma will be monitored A 56 LEU CG mod.= -0.32 id.= -2.59 dev= -2.273 sig.= 0.200 A 98 ILE CB mod.= -0.70 id.= 2.64 dev= 3.349 sig.= 0.200 A 124 ILE CB mod.= -0.33 id.= 2.64 dev= 2.971 sig.= 0.200 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 15 HIS CD2 deviation= -0.29 sigma.= 0.02 Atom: A 15 HIS HD2 deviation= 0.23 sigma.= 0.02 Atom: A 34 PHE CD2 deviation= 0.22 sigma.= 0.02 Atom: A 34 PHE HD2 deviation= -0.22 sigma.= 0.02 Limits of asymmetric unit : 1.00 1.00 0.13 Grid spacing to be used : 192 192 96 Maximuum H,K,L : 58 58 27 Minimum acceptable grid spacing: 128 128 60 Limits of asymmetric unit : 1.00 1.00 0.13 Grid spacing to be used : 192 192 96 Maximuum H,K,L : 58 58 27 Minimum acceptable grid spacing: 128 128 60 fast hessian tabulation Weight matrix 0.54497236 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 80.5 Norm of Geom. positional gradient 62.4 Norm of X_ray B-factor gradient 513. Norm of Geom. B-factor gradient 0.157E+04 Product of X_ray and Geom posit. gradients -0.805E+07 Cosine of angle between them -0.308 Product of X_ray and Geom B-fact gradients -0.386E+07 Cosine of angle between them -0.003 Residuals: XRAY= 0.1249E+07 GEOM= 9770. TOTAL= 0.1259E+07 function value 1258878.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.021 0.019 Bond distances: others 814 0.000 0.020 Bond angles : refined atoms 1255 2.478 1.916 Bond angles : others 1849 4.518 3.009 Torsion angles, period 1. refined 127 7.071 5.000 Torsion angles, period 2. refined 38 36.966 23.421 Torsion angles, period 3. refined 138 16.960 15.000 Torsion angles, period 3. others 8 47.937 15.000 Torsion angles, period 4. refined 7 24.901 15.000 Chiral centres: refined atoms 132 0.461 0.200 Planar groups: refined atoms 1106 0.017 0.020 Planar groups: others 217 0.032 0.020 VDW repulsions: refined_atoms 204 0.240 0.200 VDW repulsions.others 750 0.235 0.200 VDW; torsion: refined_atoms 454 0.189 0.200 VDW; torsion.others 498 0.129 0.200 HBOND: refined_atoms 10 0.060 0.200 VDW repulsions: symmetry: refined_atoms 15 0.306 0.200 VDW repulsions: symmetry: others 35 0.483 0.200 M. chain bond B values: refined atoms 513 0.867 1.268 M. chain bond B values: others 512 0.866 1.266 M. chain angle B values: refined atoms 638 1.472 1.896 M. chain angle B values: others 639 1.471 1.898 S. chain bond B values: refined atoms 418 0.997 1.260 S. chain bond B values: others 417 0.993 1.258 S. chain angle B values: refined atoms 616 1.625 1.863 S. chain angle B values: others 616 1.625 1.861 Long range B values: refined atoms 1041 2.092 9.684 Long range B values: others 1042 2.091 9.694 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.960, B = -1.942 Babinet"s bulk solvent: scale = 0.297, B = 111.158 Partial structure 1: scale = 0.402, B = 19.327 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 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. v. resln :N:1,6,7,11,12: :Cycle 1. and v. resln :N:1,4,5,9,10: :Cycle 1. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 332.7 305.6 0.32 0.45 14 217.6 253.1 0.50 0.61 0.040 535 100.00 348.5 361.0 0.34 0.48 34 369.9 358.9 0.35 0.49 0.067 672 100.00 425.9 368.7 0.36 0.45 32 363.6 363.5 0.37 0.52 0.094 779 99.75 361.3 299.3 0.40 0.46 31 371.8 313.4 0.44 0.49 0.121 879 100.00 268.2 246.2 0.42 0.48 43 274.9 234.6 0.43 0.49 0.148 958 100.00 226.2 218.3 0.40 0.43 42 204.0 195.4 0.45 0.50 0.174 1040 100.00 213.8 200.2 0.38 0.40 38 225.9 234.1 0.37 0.44 0.201 1096 100.00 198.6 180.6 0.37 0.39 65 189.6 186.6 0.38 0.39 0.228 1185 100.00 181.6 165.3 0.36 0.37 56 198.0 181.8 0.28 0.28 0.255 1205 100.00 158.0 138.5 0.37 0.37 82 165.0 145.4 0.33 0.33 0.281 1298 100.00 136.3 121.4 0.38 0.37 59 134.9 116.4 0.40 0.39 0.308 1337 100.00 118.5 109.5 0.40 0.39 76 120.9 97.8 0.39 0.37 0.335 1403 100.00 107.2 97.0 0.38 0.36 88 100.8 90.9 0.41 0.37 0.362 1434 100.00 100.7 88.2 0.39 0.37 74 104.6 85.3 0.35 0.33 0.388 1507 100.00 94.7 81.5 0.36 0.34 76 90.8 84.6 0.35 0.32 0.415 1532 100.00 85.8 76.2 0.37 0.34 97 83.7 72.2 0.38 0.35 0.442 1579 100.00 80.7 71.3 0.37 0.35 92 82.0 67.3 0.38 0.37 0.469 1633 100.00 75.8 65.3 0.37 0.35 109 70.8 65.1 0.38 0.34 0.495 1576 93.50 66.8 60.2 0.40 0.37 79 72.0 65.9 0.36 0.33 0.522 1250 72.50 64.8 57.7 0.39 0.36 63 64.6 57.6 0.38 0.36 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 1. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 1. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.735 140 0.638 319 0.693 0.856 0.0405 376 0.724 159 0.635 535 0.697 0.840 0.0672 518 0.738 154 0.599 672 0.706 0.828 0.0940 623 0.632 156 0.552 779 0.616 0.819 0.1208 716 0.502 163 0.468 879 0.495 0.812 0.1475 800 0.562 158 0.455 958 0.544 0.816 0.1743 883 0.680 157 0.545 1040 0.660 0.842 0.2010 934 0.745 162 0.609 1096 0.725 0.900 0.2278 1022 0.761 163 0.671 1185 0.749 0.933 0.2546 1048 0.726 157 0.580 1205 0.707 0.927 0.2813 1136 0.654 162 0.558 1298 0.642 0.885 0.3081 1176 0.608 161 0.480 1337 0.592 0.841 0.3349 1243 0.629 160 0.531 1403 0.617 0.851 0.3616 1269 0.653 165 0.515 1434 0.637 0.879 0.3884 1347 0.689 160 0.584 1507 0.678 0.919 0.4151 1380 0.729 152 0.626 1532 0.719 0.922 0.4419 1421 0.727 158 0.629 1579 0.717 0.909 0.4687 1477 0.701 156 0.643 1633 0.695 0.908 0.4954 1447 0.687 131 0.494 1578 0.671 0.884 0.5222 1161 0.637 87 0.537 1248 0.630 0.829 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.3783 Free R factor = 0.3783 Overall weighted R factor = 0.3938 Free weighted R factor = 0.3924 Overall weighted R2 factor = 0.5046 Free weighted R2 factor = 0.5467 Overall correlation coefficient = 0.7997 Free correlation coefficient = 0.7673 Cruickshanks DPI for coordinate error= 0.1149 DPI based on free R factor = 0.1054 Overall figure of merit = 0.6619 ML based su of positional parameters = 0.0864 ML based su of thermal parameters = 2.0171 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 5.00000007E-02 Gamma decreased to 3.99999991E-02 fvalues 125441.10 9770.3867 1244094.3 1264181.4 CGMAT cycle number = 2 fast hessian tabulation Weight matrix 0.68135852 Actual weight 10.000000 is applied to the X-ray term function value 1241570.5 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.026 0.019 Bond distances: others 814 0.013 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.963, B = -0.203 Babinet"s bulk solvent: scale = 0.303, B = 111.182 Partial structure 1: scale = 0.402, B = 20.091 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3564 Free R factor = 0.3603 Overall figure of merit = 0.6881 ----------------------------------------------------------------------------- Trying gamma equal 3.99999991E-02 Gamma decreased to 3.09090894E-02 fvalues 123436.55 7329.8018 1234824.9 1241695.4 CGMAT cycle number = 3 fast hessian tabulation Weight matrix 0.71036094 Actual weight 9.0909090 is applied to the X-ray term function value 1121692.3 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.027 0.019 Bond distances: others 814 0.006 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.965, B = -0.056 Babinet"s bulk solvent: scale = 0.302, B = 111.167 Partial structure 1: scale = 0.404, B = 19.664 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3455 Free R factor = 0.3503 Overall figure of merit = 0.7043 ----------------------------------------------------------------------------- Trying gamma equal 3.09090894E-02 Gamma decreased to 2.26446260E-02 fvalues 122659.49 6613.9683 1117996.0 1121700.3 CGMAT cycle number = 4 fast hessian tabulation Weight matrix 0.68747795 Actual weight 8.2644625 is applied to the X-ray term function value 1015965.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.026 0.019 Bond distances: others 814 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.967, B = -0.061 Babinet"s bulk solvent: scale = 0.304, B = 111.171 Partial structure 1: scale = 0.404, B = 19.787 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3386 Free R factor = 0.3437 Overall figure of merit = 0.7125 ----------------------------------------------------------------------------- Trying gamma equal 2.26446260E-02 Gamma decreased to 1.51314782E-02 fvalues 122162.79 6376.7598 1013574.5 1015986.6 CGMAT cycle number = 5 fast hessian tabulation Weight matrix 0.71937925 Actual weight 8.2644625 is applied to the X-ray term function value 1012778.3 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.024 0.019 Bond distances: others 814 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.969, B = -0.031 Babinet"s bulk solvent: scale = 0.305, B = 111.182 Partial structure 1: scale = 0.405, B = 20.139 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3339 Free R factor = 0.3395 Overall figure of merit = 0.7187 ----------------------------------------------------------------------------- Trying gamma equal 1.51314782E-02 Gamma decreased to 8.30134377E-03 fvalues 121802.83 6152.0195 1010894.6 1012786.9 CGMAT cycle number = 6 fast hessian tabulation Weight matrix 0.74552453 Actual weight 8.2644625 is applied to the X-ray term function value 1010516.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.024 0.019 Bond distances: others 814 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.970, B = -0.033 Babinet"s bulk solvent: scale = 0.303, B = 111.173 Partial structure 1: scale = 0.408, B = 19.869 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3300 Free R factor = 0.3373 Overall figure of merit = 0.7230 ----------------------------------------------------------------------------- Trying gamma equal 8.30134377E-03 Gamma decreased to 2.09213095E-03 fvalues 121536.84 6091.5581 1009008.1 1010528.2 CGMAT cycle number = 7 fast hessian tabulation Weight matrix 0.76061785 Actual weight 8.2644625 is applied to the X-ray term function value 1008725.0 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.023 0.019 Bond distances: others 814 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.970, B = -0.040 Babinet"s bulk solvent: scale = 0.302, B = 111.188 Partial structure 1: scale = 0.409, B = 20.327 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3266 Free R factor = 0.3367 Overall figure of merit = 0.7253 ----------------------------------------------------------------------------- Trying gamma equal 2.09213095E-03 Gamma decreased to 0.0000000 fvalues 121324.38 6055.5215 1007548.9 1008736.3 CGMAT cycle number = 8 fast hessian tabulation Weight matrix 0.76803273 Actual weight 8.2644625 is applied to the X-ray term function value 1007343.3 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.023 0.019 Bond distances: others 814 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.971, B = -0.026 Babinet"s bulk solvent: scale = 0.304, B = 111.208 Partial structure 1: scale = 0.409, B = 20.959 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3240 Free R factor = 0.3365 Overall figure of merit = 0.7267 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 2.56579034E-02 Gamma decreased to 2.05263235E-02 fvalues 121160.24 6028.5840 1006576.6 1007352.9 CGMAT cycle number = 9 fast hessian tabulation Weight matrix 0.77950126 Actual weight 8.2644625 is applied to the X-ray term function value 1006527.7 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.023 0.019 Bond distances: others 814 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.970, B = -0.021 Babinet"s bulk solvent: scale = 0.303, B = 111.217 Partial structure 1: scale = 0.410, B = 21.209 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3224 Free R factor = 0.3366 Overall figure of merit = 0.7285 ----------------------------------------------------------------------------- Trying gamma equal 2.05263235E-02 Gamma decreased to 1.58612505E-02 fvalues 121066.49 5983.3477 1005938.9 1006532.8 CGMAT cycle number = 10 fast hessian tabulation Weight matrix 0.78214926 Actual weight 8.2644625 is applied to the X-ray term function value 1005777.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.022 0.019 Bond distances: others 814 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.970, B = -0.022 Babinet"s bulk solvent: scale = 0.303, B = 111.240 Partial structure 1: scale = 0.410, B = 21.879 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3211 Free R factor = 0.3374 Overall figure of merit = 0.7299 ----------------------------------------------------------------------------- Trying gamma equal 1.58612505E-02 Gamma decreased to 1.16202747E-02 fvalues 120978.59 5955.3633 1005292.4 1005778.4 **** Chiral volume outliers **** Chiral volume deviations from the ideal >10.000Sigma will be monitored A 98 ILE CB mod.= -1.43 id.= 2.64 dev= 4.070 sig.= 0.200 A 124 ILE CB mod.= -0.54 id.= 2.64 dev= 3.182 sig.= 0.200 Limits of asymmetric unit : 1.00 1.00 0.13 Grid spacing to be used : 192 192 96 Maximuum H,K,L : 58 58 27 Minimum acceptable grid spacing: 128 128 60 Limits of asymmetric unit : 1.00 1.00 0.13 Grid spacing to be used : 192 192 96 Maximuum H,K,L : 58 58 27 Minimum acceptable grid spacing: 128 128 60 WRITTEN OUTPUT MTZ FILE Logical Name: HKLOUT Filename: C:/SOLVE_REFINE/lizozim/mr-refine-build\r111.mtz Norm of X_ray positional gradient 0.00 Norm of Geom. positional gradient 0.00 Norm of X_ray B-factor gradient 0.00 Norm of Geom. B-factor gradient 0.00 Product of X_ray and Geom posit. gradients 0.00 Cosine of angle between them 0.000 Product of X_ray and Geom B-fact gradients 0.00 Cosine of angle between them 0.000 Residuals: XRAY= 0.9994E+06 GEOM= 5923. TOTAL= 0.1005E+07 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.022 0.019 Bond distances: others 814 0.002 0.020 Bond angles : refined atoms 1255 2.509 1.916 Bond angles : others 1849 1.343 3.009 Torsion angles, period 1. refined 127 7.287 5.000 Torsion angles, period 2. refined 38 36.897 23.421 Torsion angles, period 3. refined 138 16.695 15.000 Torsion angles, period 3. others 8 4.307 15.000 Torsion angles, period 4. refined 7 23.936 15.000 Chiral centres: refined atoms 132 0.472 0.200 Planar groups: refined atoms 1106 0.011 0.020 Planar groups: others 217 0.002 0.020 VDW repulsions: refined_atoms 215 0.243 0.200 VDW repulsions.others 810 0.194 0.200 VDW; torsion: refined_atoms 463 0.188 0.200 VDW; torsion.others 549 0.104 0.200 HBOND: refined_atoms 9 0.129 0.200 VDW repulsions: symmetry: refined_atoms 16 0.364 0.200 VDW repulsions: symmetry: others 32 0.325 0.200 M. chain bond B values: refined atoms 513 1.296 0.953 M. chain bond B values: others 512 1.275 0.948 M. chain angle B values: refined atoms 638 1.962 1.420 M. chain angle B values: others 639 1.966 1.424 S. chain bond B values: refined atoms 418 1.926 1.106 S. chain bond B values: others 417 1.920 1.101 S. chain angle B values: refined atoms 617 2.765 1.582 S. chain angle B values: others 617 2.765 1.580 Long range B values: refined atoms 1055 3.546 7.564 Long range B values: others 1056 3.549 7.583 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.970, B = -0.023 Babinet"s bulk solvent: scale = 0.302, B = 111.221 Partial structure 1: scale = 0.410, B = 21.372 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 11. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 11. v. resln :N:1,6,7,11,12: :Cycle 11. and v. resln :N:1,4,5,9,10: :Cycle 11. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 586.5 543.3 0.32 0.44 14 376.7 443.7 0.49 0.59 0.040 535 100.00 490.5 500.9 0.33 0.44 34 518.3 539.1 0.33 0.44 0.067 672 100.00 546.5 479.4 0.33 0.41 32 500.4 471.2 0.34 0.46 0.094 779 99.75 446.8 374.1 0.36 0.41 31 475.0 436.9 0.37 0.43 0.121 879 100.00 325.7 307.8 0.39 0.45 43 307.7 281.3 0.39 0.47 0.148 958 100.00 267.9 266.7 0.36 0.41 42 249.3 255.4 0.44 0.48 0.174 1040 100.00 249.0 242.6 0.32 0.35 38 265.3 277.6 0.33 0.39 0.201 1096 100.00 230.5 214.8 0.32 0.34 65 221.7 222.8 0.35 0.36 0.228 1185 100.00 208.3 195.9 0.29 0.31 56 219.4 210.5 0.25 0.26 0.255 1205 100.00 179.7 167.2 0.30 0.31 82 176.1 159.9 0.30 0.32 0.281 1298 100.00 154.0 142.0 0.31 0.31 59 148.5 141.3 0.35 0.35 0.308 1337 100.00 133.3 125.4 0.32 0.31 76 129.8 115.8 0.33 0.31 0.335 1403 100.00 119.7 111.5 0.30 0.28 88 114.0 109.7 0.33 0.29 0.362 1434 100.00 112.5 103.4 0.31 0.29 74 109.4 92.1 0.32 0.31 0.388 1507 100.00 104.8 95.1 0.29 0.27 76 100.3 99.3 0.32 0.28 0.415 1532 100.00 94.2 86.8 0.29 0.27 97 94.4 78.7 0.34 0.32 0.442 1579 100.00 88.7 81.8 0.28 0.26 92 89.9 77.6 0.32 0.31 0.469 1633 100.00 82.9 74.1 0.29 0.27 109 83.0 80.7 0.36 0.33 0.495 1576 93.50 71.9 66.8 0.29 0.26 79 75.0 71.7 0.30 0.26 0.522 1250 72.50 69.0 64.8 0.28 0.25 63 66.0 62.4 0.28 0.25 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 11. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 11. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.758 140 0.655 319 0.713 0.866 0.0405 376 0.757 159 0.670 535 0.732 0.860 0.0672 518 0.783 154 0.654 672 0.753 0.857 0.0940 623 0.706 156 0.626 779 0.690 0.853 0.1208 716 0.592 163 0.528 879 0.580 0.850 0.1475 800 0.643 158 0.529 958 0.624 0.845 0.1743 883 0.735 157 0.628 1040 0.719 0.859 0.2010 934 0.769 162 0.669 1096 0.754 0.902 0.2278 1022 0.799 163 0.708 1185 0.787 0.933 0.2546 1048 0.776 157 0.705 1205 0.767 0.936 0.2813 1136 0.712 162 0.616 1298 0.700 0.900 0.3081 1176 0.699 161 0.566 1337 0.683 0.872 0.3349 1243 0.762 160 0.659 1403 0.750 0.912 0.3616 1269 0.733 165 0.586 1434 0.716 0.907 0.3884 1347 0.748 160 0.687 1507 0.742 0.932 0.4151 1380 0.769 152 0.687 1532 0.761 0.940 0.4419 1421 0.784 158 0.686 1579 0.774 0.940 0.4687 1477 0.764 156 0.706 1633 0.759 0.943 0.4954 1447 0.749 131 0.583 1578 0.735 0.921 0.5222 1161 0.768 87 0.690 1248 0.763 0.915 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.3200 Free R factor = 0.3383 Overall weighted R factor = 0.3331 Free weighted R factor = 0.3527 Overall weighted R2 factor = 0.4481 Free weighted R2 factor = 0.4961 Overall correlation coefficient = 0.8440 Free correlation coefficient = 0.8111 Cruickshanks DPI for coordinate error= 0.0972 DPI based on free R factor = 0.0943 Overall figure of merit = 0.7304 ML based su of positional parameters = 0.0656 ML based su of thermal parameters = 1.5169 ----------------------------------------------------------------------------- Time in seconds: CPU = 0.00 Elapsed = 42.00 **** Things for loggraph, R factor and others vs cycle **** $TABLE: Rfactor analysis, stats vs cycle : $GRAPHS: vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LL vs cycle :N:1,5: :-LLfree vs cycle :N:1,6: :Geometry vs cycle:N:1,7,8,9,10,11: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.3783 0.3783 0.662 124911. 6658.6 0.0212 1.051 2.478 1.200 0.461 1 0.3564 0.3603 0.688 123424. 6604.8 0.0258 1.276 2.609 1.275 0.466 2 0.3455 0.3503 0.704 122659. 6576.0 0.0269 1.331 2.678 1.314 0.477 3 0.3386 0.3437 0.713 122160. 6557.5 0.0260 1.285 2.656 1.300 0.477 4 0.3339 0.3395 0.719 121802. 6544.5 0.0244 1.205 2.581 1.255 0.472 5 0.3300 0.3373 0.723 121535. 6536.7 0.0238 1.172 2.540 1.229 0.472 6 0.3266 0.3367 0.725 121323. 6530.8 0.0233 1.150 2.518 1.215 0.472 7 0.3240 0.3365 0.727 121159. 6527.4 0.0229 1.132 2.510 1.209 0.473 8 0.3224 0.3366 0.728 121066. 6526.2 0.0226 1.116 2.510 1.208 0.473 9 0.3211 0.3374 0.730 120979. 6525.8 0.0224 1.106 2.511 1.209 0.472 10 0.3200 0.3383 0.730 120922. 6526.0 0.0221 1.096 2.509 1.207 0.472 $$ $TEXT:Result: $$ Final results $$ Initial Final R factor 0.3783 0.3200 R free 0.3783 0.3383 Rms BondLength 0.0212 0.0221 Rms BondAngle 2.4783 2.5091 Rms ChirVolume 0.4614 0.4720 $$
Refmac_5.7.0032: End of Refmac_5.7.0032 Times: User: 0.0s System: 0.0s Elapsed: 0:53
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CCP4i: Writing final coordinates (XYZOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r111.pdb
CCP4i: Writing final phases (HKLOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r111.mtz
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