Summary:
Initial | After 15 cycles | |
---|---|---|
R factor | 0.2270 | 0.1916 |
Rfree | 0.2461 | 0.2115 |
RMSD Bond Length | 0.0227 | 0.0202 |
RMSD Bond Angle | 2.130 | 2.078 |
RMSD Chiral Centre | 0.143 | 0.150 |
Result:
Initial | Final | |
---|---|---|
R factor | 0.2270 | 0.1916 |
R free | 0.2461 | 0.2115 |
Rms BondLength | 0.0227 | 0.0202 |
Rms BondAngle | 2.1303 | 2.0777 |
Rms ChirVolume | 0.1427 | 0.1498 |
Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 16. Rfactor analysis, F distribution v resln Cycle 16. 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: 19:50:58 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 15 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--- temp 0.8 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\r211-coot-1.pdb Output coordinate file. Logical name - XYZOUT actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r31.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\r31.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 : 15 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= 0.80 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\r211-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 : 1061 Number of residues : 195 Number of chains : 2 I am reading library. Please wait. mon_lib.cif WARNING : link:SS is found dist = 2.046 ideal_dist= 2.031 ch:AA res: 6 CYS at:SG .->AA res: 127 CYS at:SG . WARNING : link:SS is found dist = 2.063 ideal_dist= 2.031 ch:AA res: 30 CYS at:SG .->AA res: 115 CYS at:SG . WARNING : link:SS is found dist = 2.061 ideal_dist= 2.031 ch:AA res: 64 CYS at:SG .->AA res: 80 CYS at:SG . WARNING : link:SS is found dist = 2.044 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: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:CG GLN 121 AA is missing in the structure ATTENTION: atom:CD GLN 121 AA is missing in the structure ATTENTION: atom:OE1 GLN 121 AA is missing in the structure ATTENTION: atom:NE2 GLN 121 AA is missing in the structure Number of chains : 2 Total number of monomers : 195 Number of atoms : 2176 Number of missing atoms : 10 Number of rebuilt atoms : 960 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: 1958 0 1958 Angles: 3511 0 3511 Chirals: 145 0 145 Planes: 324 0 324 Torsions: 813 0 813 --------------------------------------- **** 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 Atom (C 41 O)"s total occupancy (occ*multipl) > 1.0. Changing it **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 61 ARG C . - A 62 TRP N . mod.= 1.482 id.= 1.329 dev= -0.153 sig.= 0.014 A 128 ARG C . - A 129 LEU N . mod.= 1.153 id.= 1.329 dev= 0.176 sig.= 0.014 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 1.9489247 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 74.3 Norm of Geom. positional gradient 66.5 Norm of X_ray B-factor gradient 353. Norm of Geom. B-factor gradient 121. Product of X_ray and Geom posit. gradients -0.116E+08 Cosine of angle between them -0.393 Product of X_ray and Geom B-fact gradients -0.360E+08 Cosine of angle between them -0.420 Residuals: XRAY= 0.1156E+07 GEOM= 6720. TOTAL= 0.1162E+07 function value 1162250.4 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.023 0.019 Bond distances: others 938 0.000 0.020 Bond angles : refined atoms 1385 2.130 1.900 Bond angles : others 2126 3.889 3.008 Torsion angles, period 1. refined 130 6.139 5.000 Torsion angles, period 2. refined 49 37.564 23.265 Torsion angles, period 3. refined 162 12.382 15.000 Torsion angles, period 3. others 8 48.004 15.000 Torsion angles, period 4. refined 10 22.766 15.000 Chiral centres: refined atoms 145 0.143 0.200 Planar groups: refined atoms 1204 0.012 0.020 Planar groups: others 268 0.022 0.020 VDW repulsions: refined_atoms 285 0.264 0.200 VDW repulsions.others 832 0.236 0.200 VDW; torsion: refined_atoms 515 0.187 0.200 VDW; torsion.others 514 0.112 0.200 HBOND: refined_atoms 20 0.127 0.200 HBOND.others 1 0.002 0.200 VDW repulsions: symmetry: refined_atoms 10 0.178 0.200 VDW repulsions: symmetry: others 18 0.152 0.200 HBOND: symmetry: refined_atoms 2 0.137 0.200 M. chain bond B values: refined atoms 517 1.236 0.929 M. chain bond B values: others 516 1.237 0.925 M. chain angle B values: refined atoms 645 1.774 1.392 M. chain angle B values: others 646 1.773 1.397 S. chain bond B values: refined atoms 503 1.808 1.102 S. chain bond B values: others 504 1.806 1.104 S. chain angle B values: refined atoms 739 2.672 1.590 S. chain angle B values: others 740 2.670 1.592 Long range B values: refined atoms 1264 5.062 8.431 Long range B values: others 1242 5.114 8.045 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.945, B = -0.257 Babinet"s bulk solvent: scale = 0.218, B = 132.106 Partial structure 1: scale = 0.435, B = 27.064 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 337.8 322.2 0.22 0.31 14 221.0 231.6 0.30 0.38 0.040 535 100.00 353.8 375.8 0.22 0.30 34 375.6 430.7 0.24 0.37 0.067 672 100.00 432.4 408.1 0.20 0.27 32 369.2 368.7 0.20 0.26 0.094 779 99.75 366.8 334.0 0.23 0.28 31 377.5 342.1 0.21 0.23 0.121 879 100.00 272.3 264.9 0.24 0.29 43 279.1 269.7 0.23 0.29 0.148 958 100.00 229.7 234.2 0.25 0.28 42 207.2 218.8 0.28 0.32 0.174 1040 100.00 217.0 215.2 0.22 0.25 38 229.4 232.3 0.21 0.26 0.201 1096 100.00 201.7 189.5 0.23 0.25 65 192.5 188.9 0.31 0.33 0.228 1185 100.00 184.4 178.4 0.22 0.24 56 201.1 195.5 0.23 0.25 0.255 1205 100.00 160.4 155.0 0.23 0.23 82 167.5 163.8 0.22 0.23 0.281 1298 100.00 138.4 132.4 0.24 0.24 59 136.9 133.2 0.27 0.28 0.308 1337 100.00 120.3 117.6 0.23 0.22 76 122.7 114.9 0.25 0.25 0.335 1403 100.00 108.9 104.4 0.23 0.22 88 102.4 101.9 0.28 0.25 0.362 1434 100.00 102.2 96.8 0.22 0.21 74 106.2 95.2 0.22 0.21 0.388 1507 100.00 96.2 91.1 0.22 0.21 76 92.2 86.0 0.25 0.23 0.415 1532 100.00 87.1 82.6 0.22 0.20 97 84.9 75.7 0.27 0.25 0.442 1579 100.00 82.0 78.1 0.21 0.19 92 83.3 77.6 0.26 0.24 0.469 1633 100.00 77.0 72.0 0.22 0.21 109 71.9 70.6 0.24 0.22 0.495 1576 93.50 67.8 64.7 0.24 0.21 79 73.1 69.4 0.28 0.24 0.522 1250 72.50 65.8 63.8 0.23 0.21 63 65.6 62.7 0.26 0.23 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.897 140 0.814 319 0.860 0.947 0.0405 376 0.911 159 0.808 535 0.881 0.964 0.0672 518 0.922 154 0.804 672 0.895 0.978 0.0940 623 0.903 156 0.833 779 0.889 0.988 0.1208 716 0.849 163 0.742 879 0.829 0.991 0.1475 800 0.854 158 0.713 958 0.830 0.955 0.1743 883 0.865 157 0.736 1040 0.845 0.940 0.2010 934 0.851 162 0.727 1096 0.832 0.962 0.2278 1022 0.869 163 0.773 1185 0.856 0.968 0.2546 1048 0.860 157 0.812 1205 0.854 0.963 0.2813 1136 0.833 162 0.732 1298 0.821 0.950 0.3081 1176 0.825 161 0.691 1337 0.808 0.944 0.3349 1243 0.847 160 0.773 1403 0.838 0.962 0.3616 1269 0.841 165 0.705 1434 0.825 0.968 0.3884 1347 0.840 160 0.782 1507 0.834 0.973 0.4151 1380 0.841 152 0.762 1532 0.833 0.967 0.4419 1421 0.866 158 0.792 1579 0.858 0.978 0.4687 1477 0.839 156 0.771 1633 0.833 0.969 0.4954 1447 0.812 131 0.668 1578 0.800 0.952 0.5222 1161 0.818 87 0.751 1248 0.813 0.936 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.2270 Free R factor = 0.2461 Overall weighted R factor = 0.2413 Free weighted R factor = 0.2630 Overall weighted R2 factor = 0.3132 Free weighted R2 factor = 0.3519 Overall correlation coefficient = 0.9305 Free correlation coefficient = 0.9175 Cruickshanks DPI for coordinate error= 0.0753 DPI based on free R factor = 0.0738 Overall figure of merit = 0.8368 ML based su of positional parameters = 0.0462 ML based su of thermal parameters = 1.0986 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 5.00000007E-02 Gamma decreased to 3.99999991E-02 fvalues 115582.70 6719.9487 1147391.8 1162546.9 CGMAT cycle number = 2 fast hessian tabulation Weight matrix 2.3758512 Actual weight 10.000000 is applied to the X-ray term function value 1143870.9 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.021 0.019 Bond distances: others 938 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.938, B = -0.249 Babinet"s bulk solvent: scale = 0.186, B = 132.102 Partial structure 1: scale = 0.442, B = 26.910 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.2101 Free R factor = 0.2297 Overall figure of merit = 0.8541 ----------------------------------------------------------------------------- Trying gamma equal 3.99999991E-02 Gamma decreased to 3.09090894E-02 fvalues 113953.98 4996.6016 1133236.9 1144536.4 CGMAT cycle number = 3 fast hessian tabulation Weight matrix 2.8814058 Actual weight 10.000000 is applied to the X-ray term function value 1129014.1 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.022 0.019 Bond distances: others 938 0.005 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.933, B = -0.008 Babinet"s bulk solvent: scale = 0.165, B = 132.088 Partial structure 1: scale = 0.444, B = 25.965 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1985 Free R factor = 0.2182 Overall figure of merit = 0.8683 ----------------------------------------------------------------------------- Trying gamma equal 3.09090894E-02 Gamma decreased to 2.26446260E-02 fvalues 112421.07 4800.3296 1125629.0 1129011.0 CGMAT cycle number = 4 fast hessian tabulation Weight matrix 2.7534881 Actual weight 9.0909090 is applied to the X-ray term function value 1022965.0 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.023 0.019 Bond distances: others 938 0.005 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.932, B = -0.015 Babinet"s bulk solvent: scale = 0.161, B = 132.085 Partial structure 1: scale = 0.444, B = 25.702 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1947 Free R factor = 0.2146 Overall figure of merit = 0.8724 ----------------------------------------------------------------------------- Trying gamma equal 2.26446260E-02 Gamma decreased to 1.51314782E-02 fvalues 111974.84 5018.1328 1021404.1 1022971.3 CGMAT cycle number = 5 fast hessian tabulation Weight matrix 2.5653701 Actual weight 8.2644625 is applied to the X-ray term function value 928673.50 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.023 0.019 Bond distances: others 938 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.932, B = 0.007 Babinet"s bulk solvent: scale = 0.159, B = 132.080 Partial structure 1: scale = 0.444, B = 25.350 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1929 Free R factor = 0.2133 Overall figure of merit = 0.8745 ----------------------------------------------------------------------------- Trying gamma equal 1.51314782E-02 Gamma decreased to 8.30134377E-03 fvalues 111766.59 4984.0449 927906.06 928674.81 CGMAT cycle number = 6 fast hessian tabulation Weight matrix 2.5876088 Actual weight 8.2644625 is applied to the X-ray term function value 927867.19 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.022 0.019 Bond distances: others 938 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.932, B = 0.002 Babinet"s bulk solvent: scale = 0.157, B = 132.080 Partial structure 1: scale = 0.444, B = 25.356 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1921 Free R factor = 0.2125 Overall figure of merit = 0.8755 ----------------------------------------------------------------------------- Trying gamma equal 8.30134377E-03 Gamma decreased to 2.09213095E-03 fvalues 111683.58 4862.0029 927479.06 927866.75 CGMAT cycle number = 7 fast hessian tabulation Weight matrix 2.5986452 Actual weight 8.2644625 is applied to the X-ray term function value 927481.94 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.022 0.019 Bond distances: others 938 0.005 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.932, B = 0.002 Babinet"s bulk solvent: scale = 0.157, B = 132.080 Partial structure 1: scale = 0.444, B = 25.356 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1916 Free R factor = 0.2122 Overall figure of merit = 0.8759 ----------------------------------------------------------------------------- Trying gamma equal 2.09213095E-03 Gamma decreased to 0.0000000 fvalues 111634.84 4878.2988 927231.19 927480.25 CGMAT cycle number = 8 fast hessian tabulation Weight matrix 2.5922587 Actual weight 8.2644625 is applied to the X-ray term function value 927330.25 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.022 0.019 Bond distances: others 938 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.932, B = 0.005 Babinet"s bulk solvent: scale = 0.155, B = 132.080 Partial structure 1: scale = 0.445, B = 25.300 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1914 Free R factor = 0.2120 Overall figure of merit = 0.8760 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 2.56579034E-02 Gamma decreased to 2.05263235E-02 fvalues 111620.23 4851.0391 927174.69 927332.25 CGMAT cycle number = 9 fast hessian tabulation Weight matrix 2.5986683 Actual weight 8.2644625 is applied to the X-ray term function value 927210.13 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.022 0.019 Bond distances: others 938 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.932, B = 0.006 Babinet"s bulk solvent: scale = 0.154, B = 132.076 Partial structure 1: scale = 0.444, B = 25.018 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1912 Free R factor = 0.2120 Overall figure of merit = 0.8762 ----------------------------------------------------------------------------- Trying gamma equal 2.05263235E-02 Gamma decreased to 1.58612505E-02 fvalues 111607.14 4837.7529 927135.75 927210.75 CGMAT cycle number = 10 fast hessian tabulation Weight matrix 2.5941525 Actual weight 8.2644625 is applied to the X-ray term function value 927220.81 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.022 0.019 Bond distances: others 938 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.932, B = -0.003 Babinet"s bulk solvent: scale = 0.153, B = 132.076 Partial structure 1: scale = 0.444, B = 25.047 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1911 Free R factor = 0.2119 Overall figure of merit = 0.8761 ----------------------------------------------------------------------------- Trying gamma equal 1.58612505E-02 Gamma decreased to 1.16202747E-02 fvalues 111606.55 4853.2490 927151.50 927221.44 CGMAT cycle number = 11 fast hessian tabulation Weight matrix 2.3555946 Actual weight 7.5131474 is applied to the X-ray term function value 843354.38 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.022 0.019 Bond distances: others 938 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.932, B = -0.004 Babinet"s bulk solvent: scale = 0.153, B = 132.078 Partial structure 1: scale = 0.445, B = 25.166 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1911 Free R factor = 0.2118 Overall figure of merit = 0.8761 ----------------------------------------------------------------------------- Trying gamma equal 1.16202747E-02 Gamma decreased to 7.76484236E-03 fvalues 111607.09 4833.6514 843324.13 843354.19 CGMAT cycle number = 12 fast hessian tabulation Weight matrix 2.1402354 Actual weight 6.8301339 is applied to the X-ray term function value 767132.94 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.021 0.019 Bond distances: others 938 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.932, B = -0.006 Babinet"s bulk solvent: scale = 0.152, B = 132.079 Partial structure 1: scale = 0.445, B = 25.295 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1912 Free R factor = 0.2118 Overall figure of merit = 0.8761 ----------------------------------------------------------------------------- Trying gamma equal 7.76484236E-03 Gamma decreased to 4.25990392E-03 fvalues 111628.72 4694.4741 767122.56 767133.56 CGMAT cycle number = 13 fast hessian tabulation Weight matrix 2.1385775 Actual weight 6.8301339 is applied to the X-ray term function value 767164.25 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.020 0.019 Bond distances: others 938 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.931, B = -0.006 Babinet"s bulk solvent: scale = 0.151, B = 132.080 Partial structure 1: scale = 0.445, B = 25.356 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1915 Free R factor = 0.2116 Overall figure of merit = 0.8762 ----------------------------------------------------------------------------- Trying gamma equal 4.25990392E-03 Gamma decreased to 1.07359642E-03 fvalues 111658.71 4521.2886 767140.00 767165.25 CGMAT cycle number = 14 fast hessian tabulation Weight matrix 2.1345587 Actual weight 6.8301339 is applied to the X-ray term function value 767161.69 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.020 0.019 Bond distances: others 938 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.931, B = -0.000 Babinet"s bulk solvent: scale = 0.151, B = 132.080 Partial structure 1: scale = 0.445, B = 25.358 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1916 Free R factor = 0.2115 Overall figure of merit = 0.8761 ----------------------------------------------------------------------------- Trying gamma equal 1.07359642E-03 Gamma decreased to 0.0000000 fvalues 111669.45 4444.4448 767239.75 767161.75 fvalues 111669.45 4444.4448 767198.56 767161.75 CGMAT cycle number = 15 fast hessian tabulation Weight matrix 2.1379151 Actual weight 6.8301339 is applied to the X-ray term function value 767172.31 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.020 0.019 Bond distances: others 938 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.931, B = -0.006 Babinet"s bulk solvent: scale = 0.151, B = 132.080 Partial structure 1: scale = 0.445, B = 25.350 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.1916 Free R factor = 0.2115 Overall figure of merit = 0.8762 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 1.31665589E-02 Gamma decreased to 1.05332471E-02 fvalues 111671.73 4440.7930 767175.25 767173.69 fvalues 111671.73 4440.7930 767170.88 767173.69 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\r31.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= 0.7628E+06 GEOM= 4425. TOTAL= 0.7672E+06 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1020 0.020 0.019 Bond distances: others 938 0.002 0.020 Bond angles : refined atoms 1385 2.078 1.900 Bond angles : others 2126 1.023 3.008 Torsion angles, period 1. refined 130 6.360 5.000 Torsion angles, period 2. refined 49 37.332 23.265 Torsion angles, period 3. refined 162 12.108 15.000 Torsion angles, period 3. others 8 14.191 15.000 Torsion angles, period 4. refined 10 22.844 15.000 Chiral centres: refined atoms 145 0.150 0.200 Planar groups: refined atoms 1204 0.011 0.020 Planar groups: others 268 0.001 0.020 VDW repulsions: refined_atoms 274 0.266 0.200 VDW repulsions.others 874 0.175 0.200 VDW; torsion: refined_atoms 517 0.186 0.200 VDW; torsion.others 562 0.088 0.200 HBOND: refined_atoms 15 0.154 0.200 VDW repulsions: symmetry: refined_atoms 11 0.183 0.200 VDW repulsions: symmetry: others 18 0.125 0.200 HBOND: symmetry: refined_atoms 1 0.175 0.200 M. chain bond B values: refined atoms 517 1.201 0.912 M. chain bond B values: others 516 1.159 0.908 M. chain angle B values: refined atoms 645 1.735 1.369 M. chain angle B values: others 646 1.738 1.372 S. chain bond B values: refined atoms 503 2.049 1.100 S. chain bond B values: others 504 2.047 1.102 S. chain angle B values: refined atoms 739 2.895 1.575 S. chain angle B values: others 740 2.893 1.577 Long range B values: refined atoms 1245 3.461 7.724 Long range B values: others 1223 3.458 7.625 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.931, B = -0.006 Babinet"s bulk solvent: scale = 0.151, B = 132.081 Partial structure 1: scale = 0.445, B = 25.410 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.28 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 16. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 16. v. resln :N:1,6,7,11,12: :Cycle 16. and v. resln :N:1,4,5,9,10: :Cycle 16. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 611.1 590.5 0.21 0.29 14 392.5 412.2 0.25 0.32 0.040 535 100.00 511.1 536.2 0.20 0.27 34 540.1 608.1 0.22 0.35 0.067 672 100.00 569.5 538.8 0.19 0.25 32 521.5 528.3 0.22 0.28 0.094 779 99.75 465.6 429.2 0.22 0.26 31 495.0 449.3 0.20 0.21 0.121 879 100.00 339.4 333.2 0.22 0.26 43 320.7 315.1 0.22 0.29 0.148 958 100.00 279.2 288.7 0.22 0.25 42 259.8 266.4 0.26 0.30 0.174 1040 100.00 259.5 261.5 0.19 0.22 38 276.5 290.8 0.16 0.19 0.201 1096 100.00 240.2 230.0 0.19 0.20 65 231.0 232.4 0.20 0.22 0.228 1185 100.00 217.1 212.8 0.18 0.19 56 228.6 222.7 0.16 0.17 0.255 1205 100.00 187.2 181.8 0.18 0.19 82 183.5 182.2 0.21 0.22 0.281 1298 100.00 160.5 156.4 0.19 0.19 59 154.7 153.8 0.22 0.22 0.308 1337 100.00 138.9 137.7 0.19 0.18 76 135.3 133.2 0.21 0.21 0.335 1403 100.00 124.8 121.7 0.18 0.18 88 118.8 119.0 0.25 0.24 0.362 1434 100.00 117.2 111.3 0.18 0.17 74 114.0 104.2 0.22 0.21 0.388 1507 100.00 109.2 105.2 0.17 0.16 76 104.6 100.9 0.21 0.20 0.415 1532 100.00 98.2 93.8 0.17 0.15 97 98.4 90.0 0.21 0.19 0.442 1579 100.00 92.4 88.0 0.17 0.16 92 93.7 87.1 0.20 0.20 0.469 1633 100.00 86.4 82.1 0.17 0.15 109 86.5 82.3 0.23 0.21 0.495 1576 93.50 74.9 72.4 0.18 0.16 79 78.2 73.9 0.22 0.19 0.522 1250 72.50 71.9 69.8 0.18 0.15 63 68.8 64.5 0.22 0.19 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 16. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 16. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.906 140 0.819 319 0.868 0.964 0.0405 376 0.919 159 0.826 535 0.891 0.976 0.0672 518 0.933 154 0.826 672 0.908 0.984 0.0940 623 0.917 156 0.856 779 0.905 0.991 0.1208 716 0.863 163 0.762 879 0.845 0.991 0.1475 800 0.874 158 0.758 958 0.855 0.955 0.1743 883 0.896 157 0.790 1040 0.880 0.943 0.2010 934 0.911 162 0.840 1096 0.901 0.974 0.2278 1022 0.926 163 0.864 1185 0.918 0.983 0.2546 1048 0.898 157 0.832 1205 0.890 0.975 0.2813 1136 0.866 162 0.782 1298 0.856 0.961 0.3081 1176 0.878 161 0.771 1337 0.865 0.956 0.3349 1243 0.878 160 0.803 1403 0.869 0.966 0.3616 1269 0.865 165 0.722 1434 0.848 0.980 0.3884 1347 0.880 160 0.841 1507 0.876 0.987 0.4151 1380 0.890 152 0.788 1532 0.880 0.983 0.4419 1421 0.896 158 0.823 1579 0.889 0.992 0.4687 1477 0.883 156 0.826 1633 0.877 0.985 0.4954 1447 0.862 131 0.741 1578 0.852 0.975 0.5222 1161 0.885 87 0.800 1248 0.879 0.973 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.1916 Free R factor = 0.2115 Overall weighted R factor = 0.2027 Free weighted R factor = 0.2266 Overall weighted R2 factor = 0.2718 Free weighted R2 factor = 0.3108 Overall correlation coefficient = 0.9469 Free correlation coefficient = 0.9362 Cruickshanks DPI for coordinate error= 0.0635 DPI based on free R factor = 0.0634 Overall figure of merit = 0.8762 ML based su of positional parameters = 0.0365 ML based su of thermal parameters = 0.8623 ----------------------------------------------------------------------------- Time in seconds: CPU = 0.00 Elapsed = 65.00 **** 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: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.2270 0.2461 0.837 115553. 6276.8 0.0227 1.211 2.130 1.077 0.143 1 0.2101 0.2297 0.854 113887. 6199.9 0.0215 1.113 2.128 1.072 0.142 2 0.1985 0.2182 0.868 112421. 6129.7 0.0225 1.151 2.213 1.117 0.153 3 0.1947 0.2146 0.872 111974. 6108.6 0.0234 1.200 2.268 1.148 0.162 4 0.1929 0.2133 0.874 111766. 6098.0 0.0230 1.181 2.252 1.139 0.162 5 0.1921 0.2125 0.875 111684. 6093.3 0.0223 1.141 2.210 1.115 0.160 6 0.1916 0.2122 0.876 111635. 6091.7 0.0222 1.136 2.201 1.110 0.160 7 0.1914 0.2120 0.876 111620. 6091.8 0.0222 1.136 2.197 1.108 0.160 8 0.1912 0.2120 0.876 111607. 6091.9 0.0222 1.136 2.195 1.108 0.160 9 0.1911 0.2119 0.876 111606. 6092.3 0.0222 1.137 2.195 1.108 0.160 10 0.1911 0.2118 0.876 111607. 6092.8 0.0222 1.137 2.194 1.108 0.160 11 0.1912 0.2118 0.876 111629. 6093.0 0.0214 1.094 2.152 1.084 0.156 12 0.1915 0.2116 0.876 111659. 6092.9 0.0205 1.044 2.100 1.055 0.152 13 0.1916 0.2115 0.876 111669. 6092.8 0.0202 1.033 2.083 1.046 0.150 14 0.1916 0.2115 0.876 111672. 6092.9 0.0202 1.032 2.081 1.045 0.150 15 0.1916 0.2115 0.876 111676. 6093.2 0.0202 1.030 2.078 1.043 0.150 $$ $TEXT:Result: $$ Final results $$ Initial Final R factor 0.2270 0.1916 R free 0.2461 0.2115 Rms BondLength 0.0227 0.0202 Rms BondAngle 2.1303 2.0777 Rms ChirVolume 0.1427 0.1498 $$
Refmac_5.7.0032: End of Refmac_5.7.0032 Times: User: 0.0s System: 0.0s Elapsed: 1:17
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CCP4i: Writing final coordinates (XYZOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r31.pdb
CCP4i: Writing final phases (HKLOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r31.mtz
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