Summary:
Initial | After 10 cycles | |
---|---|---|
R factor | 0.2959 | 0.2612 |
Rfree | 0.3120 | 0.2788 |
RMSD Bond Length | 0.0458 | 0.0240 |
RMSD Bond Angle | 3.042 | 2.341 |
RMSD Chiral Centre | 0.168 | 0.148 |
Result:
Initial | Final | |
---|---|---|
R factor | 0.2959 | 0.2612 |
R free | 0.3120 | 0.2788 |
Rms BondLength | 0.0458 | 0.0240 |
Rms BondAngle | 3.0418 | 2.3411 |
Rms ChirVolume | 0.1676 | 0.1477 |
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 |
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
############################################################### ############################################################### ############################################################### ### CCP4 6.3: Refmac_5.7.0032 version 5.7.0032 : 05/09/12## ############################################################### User: Administrator Run date: 10/ 5/2013 Run time: 19:19:15 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\r111-coot-1.pdb Output coordinate file. Logical name - XYZOUT actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r21.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\r21.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\r111-coot-1.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 : 951 Number of residues : 128 Number of chains : 1 I am reading library. Please wait. mon_lib.cif WARNING : link:SS is found dist = 3.171 ideal_dist= 2.031 ch:AA res: 6 CYS at:SG .->AA res: 127 CYS at:SG . WARNING : link:SS is found dist = 2.072 ideal_dist= 2.031 ch:AA res: 30 CYS at:SG .->AA res: 115 CYS at:SG . WARNING : link:SS is found dist = 2.046 ideal_dist= 2.031 ch:AA res: 64 CYS at:SG .->AA res: 80 CYS at:SG . WARNING : link:SS is found dist = 2.049 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 LYS 13 AA is missing in the structure ATTENTION: atom:NZ LYS 13 AA is missing in the structure ATTENTION: atom:CG ARG 14 AA is missing in the structure ATTENTION: atom:CD ARG 14 AA is missing in the structure ATTENTION: atom:NE ARG 14 AA is missing in the structure ATTENTION: atom:CZ ARG 14 AA is missing in the structure ATTENTION: atom:NH1 ARG 14 AA is missing in the structure ATTENTION: atom:NH2 ARG 14 AA is missing in the structure ATTENTION: atom:CD ARG 45 AA is missing in the structure ATTENTION: atom:NE ARG 45 AA is missing in the structure ATTENTION: atom:CZ ARG 45 AA is missing in the structure ATTENTION: atom:NH1 ARG 45 AA is missing in the structure ATTENTION: atom:NH2 ARG 45 AA is missing in the structure ATTENTION: atom:CG TRP 62 AA is missing in the structure ATTENTION: atom:CD1 TRP 62 AA is missing in the structure ATTENTION: atom:NE1 TRP 62 AA is missing in the structure ATTENTION: atom:CE2 TRP 62 AA is missing in the structure ATTENTION: atom:CD2 TRP 62 AA is missing in the structure ATTENTION: atom:CE3 TRP 62 AA is missing in the structure ATTENTION: atom:CZ3 TRP 62 AA is missing in the structure ... and more ... Number of chains : 1 Total number of monomers : 128 Number of atoms : 1949 Number of missing atoms : 41 Number of rebuilt atoms : 904 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: 1850 0 1850 Angles: 3312 0 3312 Chirals: 142 0 142 Planes: 313 0 313 Torsions: 762 0 762 --------------------------------------- **** 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 distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 6 CYS SG . - A 127 CYS SG . mod.= 3.171 id.= 2.031 dev= -1.140 sig.= 0.020 A 33 LYS C . - A 34 PHE N . mod.= 1.515 id.= 1.329 dev= -0.186 sig.= 0.014 A 72 SER C . - A 73 ARG N . mod.= 1.160 id.= 1.329 dev= 0.169 sig.= 0.014 A 104 GLY C . - A 105 MET N . mod.= 1.485 id.= 1.329 dev= -0.156 sig.= 0.014 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 127 CYS CB - A 6 CYS SG mod.= 41.31 id.= 103.80 dev= 62.487 sig.= 1.800 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 0.99270660 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 84.7 Norm of Geom. positional gradient 100. Norm of X_ray B-factor gradient 564. Norm of Geom. B-factor gradient 359. Product of X_ray and Geom posit. gradients -0.351E+07 Cosine of angle between them -0.075 Product of X_ray and Geom B-fact gradients -0.146E+08 Cosine of angle between them -0.039 Residuals: XRAY= 0.1198E+07 GEOM= 0.1418E+05 TOTAL= 0.1212E+07 function value 1212463.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.046 0.019 Bond distances: others 877 0.000 0.020 Bond angles : refined atoms 1322 3.042 1.903 Bond angles : others 1990 4.052 3.008 Torsion angles, period 1. refined 127 6.643 5.000 Torsion angles, period 2. refined 43 38.002 24.419 Torsion angles, period 3. refined 148 12.851 15.000 Torsion angles, period 3. others 8 44.182 15.000 Torsion angles, period 4. refined 6 18.345 15.000 Chiral centres: refined atoms 142 0.168 0.200 Planar groups: refined atoms 1154 0.013 0.020 Planar groups: others 242 0.023 0.020 VDW repulsions: refined_atoms 226 0.242 0.200 VDW repulsions.others 796 0.252 0.200 VDW; torsion: refined_atoms 493 0.198 0.200 VDW; torsion.others 508 0.133 0.200 HBOND: refined_atoms 12 0.151 0.200 HBOND.others 1 0.059 0.200 VDW repulsions: symmetry: refined_atoms 4 0.099 0.200 VDW repulsions: symmetry: others 12 0.146 0.200 HBOND: symmetry: refined_atoms 2 0.383 0.200 M. chain bond B values: refined atoms 511 1.434 0.953 M. chain bond B values: others 510 1.433 0.950 M. chain angle B values: refined atoms 637 2.167 1.426 M. chain angle B values: others 638 2.166 1.429 S. chain bond B values: refined atoms 462 3.161 1.276 S. chain bond B values: others 463 3.157 1.278 S. chain angle B values: refined atoms 685 4.664 1.794 S. chain angle B values: others 685 4.663 1.794 Long range B values: refined atoms 1141 4.457 8.317 Long range B values: others 1142 4.456 8.327 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.981, B = -0.108 Babinet"s bulk solvent: scale = 0.233, B = 111.471 Partial structure 1: scale = 0.454, B = 18.402 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 325.5 305.3 0.27 0.37 14 212.9 218.3 0.25 0.32 0.040 535 100.00 340.9 359.8 0.25 0.34 34 361.8 379.7 0.30 0.43 0.067 672 100.00 416.6 383.0 0.26 0.35 32 355.7 333.4 0.27 0.38 0.094 779 99.75 353.4 306.5 0.30 0.34 31 363.7 334.8 0.26 0.32 0.121 879 100.00 262.4 252.4 0.33 0.38 43 268.9 244.8 0.34 0.39 0.148 958 100.00 221.3 225.5 0.32 0.36 42 199.6 214.8 0.34 0.40 0.174 1040 100.00 209.1 203.9 0.30 0.33 38 221.0 218.8 0.30 0.35 0.201 1096 100.00 194.3 181.5 0.31 0.34 65 185.5 182.6 0.36 0.38 0.228 1185 100.00 177.7 168.1 0.29 0.30 56 193.7 180.9 0.26 0.28 0.255 1205 100.00 154.5 146.0 0.29 0.30 82 161.4 149.8 0.30 0.32 0.281 1298 100.00 133.3 124.8 0.31 0.31 59 131.9 124.9 0.32 0.33 0.308 1337 100.00 115.9 108.6 0.30 0.29 76 118.3 106.1 0.33 0.31 0.335 1403 100.00 104.9 97.8 0.30 0.29 88 98.6 96.9 0.34 0.30 0.362 1434 100.00 98.5 89.4 0.31 0.29 74 102.3 89.8 0.30 0.29 0.388 1507 100.00 92.7 83.8 0.29 0.28 76 88.8 83.7 0.31 0.28 0.415 1532 100.00 84.0 77.3 0.30 0.28 97 81.8 68.8 0.34 0.32 0.442 1579 100.00 79.0 72.5 0.29 0.27 92 80.2 69.3 0.32 0.30 0.469 1633 100.00 74.2 66.3 0.30 0.28 109 69.3 65.8 0.34 0.31 0.495 1576 93.50 65.3 60.9 0.31 0.28 79 70.4 65.9 0.34 0.29 0.522 1250 72.50 63.4 59.6 0.29 0.27 63 63.2 61.0 0.32 0.29 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.826 140 0.728 319 0.783 0.918 0.0405 376 0.844 159 0.736 535 0.812 0.927 0.0672 518 0.869 154 0.741 672 0.840 0.935 0.0940 623 0.822 156 0.742 779 0.806 0.940 0.1208 716 0.736 163 0.650 879 0.720 0.940 0.1475 800 0.758 158 0.622 958 0.736 0.912 0.1743 883 0.792 157 0.669 1040 0.774 0.904 0.2010 934 0.786 162 0.694 1096 0.772 0.932 0.2278 1022 0.817 163 0.703 1185 0.802 0.949 0.2546 1048 0.801 157 0.735 1205 0.792 0.944 0.2813 1136 0.759 162 0.652 1298 0.745 0.926 0.3081 1176 0.748 161 0.642 1337 0.735 0.918 0.3349 1243 0.762 160 0.668 1403 0.751 0.930 0.3616 1269 0.739 165 0.600 1434 0.723 0.926 0.3884 1347 0.770 160 0.722 1507 0.765 0.952 0.4151 1380 0.766 152 0.661 1532 0.756 0.941 0.4419 1421 0.794 158 0.712 1579 0.786 0.947 0.4687 1477 0.756 156 0.693 1633 0.750 0.943 0.4954 1447 0.726 131 0.559 1578 0.712 0.915 0.5222 1161 0.729 87 0.662 1248 0.725 0.903 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.2959 Free R factor = 0.3120 Overall weighted R factor = 0.3136 Free weighted R factor = 0.3314 Overall weighted R2 factor = 0.4018 Free weighted R2 factor = 0.4311 Overall correlation coefficient = 0.8830 Free correlation coefficient = 0.8628 Cruickshanks DPI for coordinate error= 0.0918 DPI based on free R factor = 0.0885 Overall figure of merit = 0.7587 ML based su of positional parameters = 0.0631 ML based su of thermal parameters = 1.4969 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 5.00000007E-02 Gamma decreased to 3.99999991E-02 fvalues 119825.60 14179.240 1191808.6 1212435.3 CGMAT cycle number = 2 fast hessian tabulation Weight matrix 1.2794142 Actual weight 10.000000 is applied to the X-ray term function value 1190577.6 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.038 0.019 Bond distances: others 877 0.008 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.968, B = -0.226 Babinet"s bulk solvent: scale = 0.201, B = 111.460 Partial structure 1: scale = 0.451, B = 17.783 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2760 Free R factor = 0.2938 Overall figure of merit = 0.7835 ----------------------------------------------------------------------------- Trying gamma equal 3.99999991E-02 Gamma decreased to 3.09090894E-02 fvalues 118395.94 6918.3716 1185818.9 1190877.8 CGMAT cycle number = 3 fast hessian tabulation Weight matrix 1.3897107 Actual weight 10.000000 is applied to the X-ray term function value 1185741.3 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.036 0.019 Bond distances: others 877 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.963, B = -0.086 Babinet"s bulk solvent: scale = 0.192, B = 111.455 Partial structure 1: scale = 0.450, B = 17.495 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2704 Free R factor = 0.2895 Overall figure of merit = 0.7913 ----------------------------------------------------------------------------- Trying gamma equal 3.09090894E-02 Gamma decreased to 2.26446260E-02 fvalues 117951.24 6299.6201 1183504.8 1185812.0 CGMAT cycle number = 4 fast hessian tabulation Weight matrix 1.4508146 Actual weight 10.000000 is applied to the X-ray term function value 1183235.0 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.034 0.019 Bond distances: others 877 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.961, B = -0.027 Babinet"s bulk solvent: scale = 0.191, B = 111.450 Partial structure 1: scale = 0.449, B = 17.208 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2679 Free R factor = 0.2868 Overall figure of merit = 0.7953 ----------------------------------------------------------------------------- Trying gamma equal 2.26446260E-02 Gamma decreased to 1.51314782E-02 fvalues 117723.08 6016.1929 1181960.3 1183247.0 CGMAT cycle number = 5 fast hessian tabulation Weight matrix 1.4735566 Actual weight 10.000000 is applied to the X-ray term function value 1181867.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.032 0.019 Bond distances: others 877 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.960, B = -0.010 Babinet"s bulk solvent: scale = 0.190, B = 111.449 Partial structure 1: scale = 0.449, B = 17.172 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2666 Free R factor = 0.2851 Overall figure of merit = 0.7971 ----------------------------------------------------------------------------- Trying gamma equal 1.51314782E-02 Gamma decreased to 8.30134377E-03 fvalues 117611.52 5764.1328 1180999.9 1181879.3 CGMAT cycle number = 6 fast hessian tabulation Weight matrix 1.4848329 Actual weight 10.000000 is applied to the X-ray term function value 1180967.1 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.029 0.019 Bond distances: others 877 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.960, B = 0.009 Babinet"s bulk solvent: scale = 0.188, B = 111.450 Partial structure 1: scale = 0.449, B = 17.231 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2657 Free R factor = 0.2842 Overall figure of merit = 0.7980 ----------------------------------------------------------------------------- Trying gamma equal 8.30134377E-03 Gamma decreased to 2.09213095E-03 fvalues 117543.80 5524.1353 1180282.1 1180962.1 CGMAT cycle number = 7 fast hessian tabulation Weight matrix 1.4868656 Actual weight 10.000000 is applied to the X-ray term function value 1180239.5 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.027 0.019 Bond distances: others 877 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.960, B = 0.012 Babinet"s bulk solvent: scale = 0.189, B = 111.453 Partial structure 1: scale = 0.449, B = 17.410 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2650 Free R factor = 0.2832 Overall figure of merit = 0.7983 ----------------------------------------------------------------------------- Trying gamma equal 2.09213095E-03 Gamma decreased to 0.0000000 fvalues 117493.41 5299.3569 1179687.9 1180233.5 CGMAT cycle number = 8 fast hessian tabulation Weight matrix 1.4925516 Actual weight 10.000000 is applied to the X-ray term function value 1179662.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.024 0.019 Bond distances: others 877 0.005 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.960, B = 0.014 Babinet"s bulk solvent: scale = 0.187, B = 111.453 Partial structure 1: scale = 0.449, B = 17.412 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2644 Free R factor = 0.2824 Overall figure of merit = 0.7986 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 2.56579034E-02 Gamma decreased to 2.05263235E-02 fvalues 117448.70 5169.5703 1179087.1 1179656.6 CGMAT cycle number = 9 fast hessian tabulation Weight matrix 1.4969430 Actual weight 10.000000 is applied to the X-ray term function value 1179089.0 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.024 0.019 Bond distances: others 877 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.960, B = 0.009 Babinet"s bulk solvent: scale = 0.185, B = 111.454 Partial structure 1: scale = 0.449, B = 17.505 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2636 Free R factor = 0.2815 Overall figure of merit = 0.7988 ----------------------------------------------------------------------------- Trying gamma equal 2.05263235E-02 Gamma decreased to 1.58612505E-02 fvalues 117400.33 5077.2466 1178132.9 1179080.5 CGMAT cycle number = 10 fast hessian tabulation Weight matrix 1.5141473 Actual weight 10.000000 is applied to the X-ray term function value 1178049.1 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.024 0.019 Bond distances: others 877 0.005 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.960, B = 0.003 Babinet"s bulk solvent: scale = 0.181, B = 111.454 Partial structure 1: scale = 0.450, B = 17.504 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2623 Free R factor = 0.2801 Overall figure of merit = 0.8000 ----------------------------------------------------------------------------- Trying gamma equal 1.58612505E-02 Gamma decreased to 1.16202747E-02 fvalues 117305.22 4992.5259 1177094.0 1178044.8 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 18 ASP CB . - A 18 ASP CG . mod.= 1.766 id.= 1.516 dev= -0.250 sig.= 0.025 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\r21.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= 0.1172E+07 GEOM= 4898. TOTAL= 0.1177E+07 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.024 0.019 Bond distances: others 877 0.007 0.020 Bond angles : refined atoms 1322 2.341 1.903 Bond angles : others 1990 1.176 3.008 Torsion angles, period 1. refined 127 6.169 5.000 Torsion angles, period 2. refined 43 38.272 24.419 Torsion angles, period 3. refined 148 14.014 15.000 Torsion angles, period 3. others 8 14.903 15.000 Torsion angles, period 4. refined 6 16.633 15.000 Chiral centres: refined atoms 142 0.148 0.200 Planar groups: refined atoms 1154 0.011 0.020 Planar groups: others 242 0.001 0.020 VDW repulsions: refined_atoms 203 0.234 0.200 VDW repulsions.others 818 0.175 0.200 VDW; torsion: refined_atoms 498 0.186 0.200 VDW; torsion.others 533 0.095 0.200 HBOND: refined_atoms 12 0.132 0.200 VDW repulsions: symmetry: refined_atoms 3 0.060 0.200 VDW repulsions: symmetry: others 12 0.113 0.200 HBOND: symmetry: refined_atoms 1 0.265 0.200 M. chain bond B values: refined atoms 511 1.060 0.913 M. chain bond B values: others 510 1.041 0.911 M. chain angle B values: refined atoms 637 1.523 1.370 M. chain angle B values: others 638 1.522 1.371 S. chain bond B values: refined atoms 462 1.636 1.018 S. chain bond B values: others 463 1.635 1.019 S. chain angle B values: refined atoms 685 2.394 1.477 S. chain angle B values: others 685 2.393 1.477 Long range B values: refined atoms 1115 2.658 7.240 Long range B values: others 1116 2.657 7.247 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.959, B = 0.015 Babinet"s bulk solvent: scale = 0.180, B = 111.455 Partial structure 1: scale = 0.451, B = 17.502 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.29 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 593.5 559.6 0.26 0.36 14 381.2 391.3 0.24 0.30 0.040 535 100.00 496.3 522.4 0.24 0.33 34 524.5 574.0 0.28 0.41 0.067 672 100.00 553.1 512.6 0.24 0.32 32 506.4 471.2 0.25 0.34 0.094 779 99.75 452.2 399.1 0.28 0.33 31 480.7 441.7 0.24 0.29 0.121 879 100.00 329.6 317.9 0.30 0.35 43 311.4 297.0 0.30 0.37 0.148 958 100.00 271.1 276.5 0.29 0.34 42 252.3 262.9 0.33 0.37 0.174 1040 100.00 252.0 247.4 0.27 0.30 38 268.5 269.1 0.28 0.33 0.201 1096 100.00 233.3 219.5 0.28 0.31 65 224.3 216.9 0.33 0.35 0.228 1185 100.00 210.8 201.6 0.26 0.28 56 222.0 213.1 0.26 0.29 0.255 1205 100.00 181.8 175.3 0.26 0.27 82 178.2 175.0 0.26 0.28 0.281 1298 100.00 155.9 148.1 0.27 0.27 59 150.3 146.5 0.31 0.31 0.308 1337 100.00 134.9 130.3 0.25 0.25 76 131.4 122.7 0.29 0.29 0.335 1403 100.00 121.2 114.7 0.25 0.24 88 115.3 113.8 0.30 0.27 0.362 1434 100.00 113.9 106.4 0.25 0.23 74 110.7 97.2 0.25 0.24 0.388 1507 100.00 106.1 99.0 0.24 0.22 76 101.5 94.4 0.25 0.23 0.415 1532 100.00 95.4 89.6 0.24 0.22 97 95.6 83.3 0.29 0.27 0.442 1579 100.00 89.8 84.5 0.23 0.21 92 91.0 83.1 0.27 0.25 0.469 1633 100.00 83.9 77.0 0.24 0.22 109 84.0 81.2 0.27 0.25 0.495 1576 93.50 72.8 68.2 0.24 0.22 79 75.9 70.8 0.29 0.25 0.522 1250 72.50 69.8 66.7 0.24 0.21 63 66.8 63.1 0.27 0.23 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.846 140 0.748 319 0.803 0.939 0.0405 376 0.865 159 0.748 535 0.830 0.941 0.0672 518 0.885 154 0.761 672 0.856 0.943 0.0940 623 0.847 156 0.775 779 0.832 0.944 0.1208 716 0.770 163 0.674 879 0.752 0.941 0.1475 800 0.781 158 0.637 958 0.757 0.912 0.1743 883 0.807 157 0.676 1040 0.787 0.904 0.2010 934 0.806 162 0.673 1096 0.786 0.932 0.2278 1022 0.837 163 0.705 1185 0.818 0.949 0.2546 1048 0.831 157 0.769 1205 0.823 0.944 0.2813 1136 0.799 162 0.675 1298 0.783 0.926 0.3081 1176 0.790 161 0.653 1337 0.774 0.921 0.3349 1243 0.812 160 0.737 1403 0.803 0.944 0.3616 1269 0.809 165 0.672 1434 0.793 0.951 0.3884 1347 0.821 160 0.775 1507 0.816 0.963 0.4151 1380 0.829 152 0.745 1532 0.821 0.960 0.4419 1421 0.854 158 0.773 1579 0.846 0.974 0.4687 1477 0.818 156 0.752 1633 0.812 0.973 0.4954 1447 0.785 131 0.640 1578 0.773 0.950 0.5222 1161 0.805 87 0.728 1248 0.800 0.938 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.2612 Free R factor = 0.2788 Overall weighted R factor = 0.2763 Free weighted R factor = 0.2981 Overall weighted R2 factor = 0.3648 Free weighted R2 factor = 0.4050 Overall correlation coefficient = 0.9031 Free correlation coefficient = 0.8861 Cruickshanks DPI for coordinate error= 0.0811 DPI based on free R factor = 0.0791 Overall figure of merit = 0.8025 ML based su of positional parameters = 0.0511 ML based su of thermal parameters = 1.1966 ----------------------------------------------------------------------------- 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: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.2959 0.3120 0.759 119828. 6460.3 0.0458 2.414 3.042 1.607 0.168 1 0.2760 0.2938 0.784 118366. 6400.2 0.0382 1.927 2.646 1.385 0.162 2 0.2704 0.2895 0.791 117944. 6381.4 0.0363 1.821 2.590 1.337 0.167 3 0.2679 0.2868 0.795 117722. 6369.5 0.0343 1.723 2.553 1.308 0.171 4 0.2666 0.2851 0.797 117610. 6363.9 0.0320 1.606 2.524 1.283 0.174 5 0.2657 0.2842 0.798 117544. 6361.4 0.0294 1.469 2.492 1.259 0.175 6 0.2650 0.2832 0.798 117494. 6359.7 0.0266 1.327 2.457 1.236 0.174 7 0.2644 0.2824 0.799 117449. 6358.4 0.0245 1.220 2.421 1.215 0.172 8 0.2636 0.2815 0.799 117401. 6357.6 0.0238 1.186 2.399 1.204 0.166 9 0.2623 0.2801 0.800 117306. 6353.0 0.0240 1.192 2.386 1.198 0.155 10 0.2612 0.2788 0.803 117189. 6345.8 0.0240 1.191 2.341 1.171 0.148 $$ $TEXT:Result: $$ Final results $$ Initial Final R factor 0.2959 0.2612 R free 0.3120 0.2788 Rms BondLength 0.0458 0.0240 Rms BondAngle 3.0418 2.3411 Rms ChirVolume 0.1676 0.1477 $$
Refmac_5.7.0032: End of Refmac_5.7.0032 Times: User: 0.0s System: 0.0s Elapsed: 0:54
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
CCP4i: Writing final coordinates (XYZOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r21.pdb
CCP4i: Writing final phases (HKLOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r21.mtz
Generated for you by baubles 0.0.8 on Fri May 10 19:20:10 2013