Summary:
Initial | After 15 cycles | |
---|---|---|
R factor | 0.1805 | 0.1637 |
Rfree | 0.2008 | 0.1914 |
RMSD Bond Length | 0.0219 | 0.0228 |
RMSD Bond Angle | 2.146 | 2.208 |
RMSD Chiral Centre | 0.133 | 0.145 |
Result:
Initial | Final | |
---|---|---|
R factor | 0.1805 | 0.1637 |
R free | 0.2008 | 0.1914 |
Rms BondLength | 0.0219 | 0.0228 |
Rms BondAngle | 2.1456 | 2.2081 |
Rms ChirVolume | 0.1332 | 0.1453 |
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: 20:38:34 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\r31-coot-1.pdb Output coordinate file. Logical name - XYZOUT actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r41.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\r41.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\r31-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 : 1123 Number of residues : 241 Number of chains : 4 I am reading library. Please wait. mon_lib.cif WARNING : link:SS is found dist = 2.038 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 . INFO: link is found (not be used) dist= 2.424 ideal_dist= 2.275 ch:AA res: 35 GLU at:OE1 .->ch:BB res: 1 NA at:NA . INFO: link is found (not be used) dist= 2.327 ideal_dist= 2.240 ch:AA res: 60 SER at:O .->ch:DD res: 1 NA at:NA . WARNING : link:SS is found dist = 2.033 ideal_dist= 2.031 ch:AA res: 64 CYS at:SG .->AA res: 80 CYS at:SG . INFO: link is found (not be used) dist= 2.387 ideal_dist= 2.240 ch:AA res: 64 CYS at:O .->ch:DD res: 1 NA at:NA . INFO: link is found (not be used) dist= 2.515 ideal_dist= 2.434 ch:AA res: 72 SER at:OG .->ch:DD res: 1 NA at:NA . INFO: link is found (not be used) dist= 2.419 ideal_dist= 2.240 ch:AA res: 73 ARG at:O .->ch:DD res: 1 NA at:NA . WARNING : link:SS is found dist = 2.034 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: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 : 4 Total number of monomers : 241 Number of atoms : 2331 Number of missing atoms : 3 Number of rebuilt atoms : 983 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 NA 4.7626 3.2850 3.1736 8.8422 1.2674 0.3136 1.1128 129.4240 0.6760 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: 1999 0 1999 Angles: 3588 0 3588 Chirals: 146 0 146 Planes: 329 0 329 Torsions: 833 0 833 --------------------------------------- **** 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 104 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 120 VAL C . - A 121 GLN N . mod.= 1.178 id.= 1.329 dev= 0.151 sig.= 0.014 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 6 CYS HB3 . - A 14 ARG HH22B mod.= 0.955 id.= 2.400 dev= -1.45 sig.= 0.20 sym.= 6 0 0 1 type = 7 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 3.2197046 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 91.2 Norm of Geom. positional gradient 69.1 Norm of X_ray B-factor gradient 386. Norm of Geom. B-factor gradient 136. Product of X_ray and Geom posit. gradients -0.171E+08 Cosine of angle between them -0.433 Product of X_ray and Geom B-fact gradients -0.494E+08 Cosine of angle between them -0.452 Residuals: XRAY= 0.1112E+07 GEOM= 7165. TOTAL= 0.1119E+07 function value 1118831.3 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.000 0.020 Bond angles : refined atoms 1408 2.146 1.903 Bond angles : others 2180 3.837 3.007 Torsion angles, period 1. refined 132 6.482 5.000 Torsion angles, period 2. refined 51 36.614 22.745 Torsion angles, period 3. refined 169 11.939 15.000 Torsion angles, period 3. others 8 49.109 15.000 Torsion angles, period 4. refined 12 21.082 15.000 Chiral centres: refined atoms 146 0.133 0.200 Planar groups: refined atoms 1225 0.012 0.020 Planar groups: others 277 0.023 0.020 VDW repulsions: refined_atoms 317 0.262 0.200 VDW repulsions.others 851 0.233 0.200 VDW; torsion: refined_atoms 523 0.186 0.200 VDW; torsion.others 533 0.106 0.200 HBOND: refined_atoms 17 0.144 0.200 Metal-ion: refined_atoms 4 0.150 0.200 VDW repulsions: symmetry: refined_atoms 23 0.301 0.200 VDW repulsions: symmetry: others 34 0.422 0.200 HBOND: symmetry: refined_atoms 1 0.175 0.200 M. chain bond B values: refined atoms 519 1.203 0.914 M. chain bond B values: others 518 1.161 0.911 M. chain angle B values: refined atoms 648 1.742 1.373 M. chain angle B values: others 649 1.746 1.376 S. chain bond B values: refined atoms 518 2.100 1.130 S. chain bond B values: others 518 2.079 1.128 S. chain angle B values: refined atoms 758 3.003 1.615 S. chain angle B values: others 758 3.003 1.613 Long range B values: refined atoms 1315 4.932 8.308 Long range B values: others 1276 4.674 7.982 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.922, B = -0.161 Babinet"s bulk solvent: scale = 0.183, B = 153.587 Partial structure 1: scale = 0.427, B = 31.969 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 346.3 334.3 0.22 0.31 14 226.5 243.7 0.20 0.26 0.040 535 100.00 362.7 383.2 0.20 0.27 34 385.0 423.6 0.21 0.33 0.067 672 100.00 443.3 420.9 0.18 0.24 32 378.5 381.4 0.18 0.23 0.094 779 99.75 376.0 350.0 0.19 0.23 31 387.0 346.4 0.20 0.22 0.121 879 100.00 279.2 273.4 0.19 0.24 43 286.2 278.1 0.18 0.24 0.148 958 100.00 235.5 242.3 0.19 0.22 42 212.4 211.3 0.22 0.26 0.174 1040 100.00 222.5 223.4 0.17 0.19 38 235.1 247.4 0.15 0.17 0.201 1096 100.00 206.7 199.4 0.17 0.18 65 197.4 195.4 0.19 0.21 0.228 1185 100.00 189.0 184.9 0.16 0.18 56 206.1 197.0 0.16 0.17 0.255 1205 100.00 164.4 159.1 0.17 0.18 82 171.7 170.8 0.21 0.22 0.281 1298 100.00 141.8 138.1 0.18 0.18 59 140.4 139.0 0.20 0.21 0.308 1337 100.00 123.4 122.1 0.18 0.18 76 125.8 122.5 0.22 0.22 0.335 1403 100.00 111.6 108.9 0.18 0.17 88 104.9 104.3 0.24 0.23 0.362 1434 100.00 104.8 100.0 0.17 0.16 74 108.9 100.2 0.20 0.19 0.388 1507 100.00 98.6 95.1 0.17 0.16 76 94.5 93.3 0.22 0.20 0.415 1532 100.00 89.3 85.9 0.17 0.16 97 87.1 79.9 0.21 0.19 0.442 1579 100.00 84.0 80.5 0.17 0.16 92 85.4 80.1 0.20 0.20 0.469 1633 100.00 78.9 75.3 0.17 0.16 109 73.7 71.9 0.23 0.20 0.495 1576 93.50 69.5 67.7 0.19 0.17 79 75.0 71.9 0.23 0.19 0.522 1250 72.50 67.4 66.0 0.18 0.16 63 67.3 62.9 0.22 0.20 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.908 140 0.835 319 0.876 0.963 0.0405 376 0.925 159 0.826 535 0.896 0.975 0.0672 518 0.938 154 0.829 672 0.913 0.984 0.0940 623 0.924 156 0.852 779 0.909 0.991 0.1208 716 0.871 163 0.769 879 0.852 0.992 0.1475 800 0.894 158 0.763 958 0.872 0.963 0.1743 883 0.921 157 0.799 1040 0.902 0.953 0.2010 934 0.922 162 0.859 1096 0.913 0.977 0.2278 1022 0.926 163 0.852 1185 0.916 0.987 0.2546 1048 0.904 157 0.828 1205 0.894 0.981 0.2813 1136 0.883 162 0.799 1298 0.873 0.969 0.3081 1176 0.884 161 0.773 1337 0.870 0.963 0.3349 1243 0.879 160 0.812 1403 0.872 0.970 0.3616 1269 0.885 165 0.746 1434 0.869 0.983 0.3884 1347 0.882 160 0.844 1507 0.878 0.985 0.4151 1380 0.890 152 0.778 1532 0.879 0.981 0.4419 1421 0.890 158 0.821 1579 0.883 0.987 0.4687 1477 0.883 156 0.831 1633 0.878 0.982 0.4954 1447 0.858 131 0.741 1578 0.848 0.967 0.5222 1161 0.879 87 0.804 1248 0.874 0.964 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.1805 Free R factor = 0.2008 Overall weighted R factor = 0.1918 Free weighted R factor = 0.2153 Overall weighted R2 factor = 0.2556 Free weighted R2 factor = 0.2850 Overall correlation coefficient = 0.9545 Free correlation coefficient = 0.9434 Cruickshanks DPI for coordinate error= 0.0620 DPI based on free R factor = 0.0619 Overall figure of merit = 0.8812 ML based su of positional parameters = 0.0367 ML based su of thermal parameters = 0.8775 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 5.00000007E-02 Gamma decreased to 3.99999991E-02 fvalues 111188.63 7165.4307 1109013.1 1119051.8 CGMAT cycle number = 2 fast hessian tabulation Weight matrix 3.5490427 Actual weight 10.000000 is applied to the X-ray term function value 1106235.4 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.921, B = -0.119 Babinet"s bulk solvent: scale = 0.175, B = 153.585 Partial structure 1: scale = 0.428, B = 31.847 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 = 0.1722 Free R factor = 0.1957 Overall figure of merit = 0.8873 ----------------------------------------------------------------------------- Trying gamma equal 3.99999991E-02 Gamma decreased to 3.09090894E-02 fvalues 110083.28 5622.7793 1099984.4 1106455.6 CGMAT cycle number = 3 fast hessian tabulation Weight matrix 3.8713167 Actual weight 10.000000 is applied to the X-ray term function value 1097749.5 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.024 0.019 Bond distances: others 962 0.005 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.920, B = -0.002 Babinet"s bulk solvent: scale = 0.168, B = 153.574 Partial structure 1: scale = 0.428, B = 31.112 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 = 0.1664 Free R factor = 0.1924 Overall figure of merit = 0.8922 ----------------------------------------------------------------------------- Trying gamma equal 3.09090894E-02 Gamma decreased to 2.26446260E-02 fvalues 109232.94 5419.9380 1096190.3 1097749.4 CGMAT cycle number = 4 fast hessian tabulation Weight matrix 3.5893137 Actual weight 9.0909090 is applied to the X-ray term function value 996621.19 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.024 0.019 Bond distances: others 962 0.006 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.920, B = -0.013 Babinet"s bulk solvent: scale = 0.168, B = 153.571 Partial structure 1: scale = 0.427, B = 30.848 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 = 0.1648 Free R factor = 0.1915 Overall figure of merit = 0.8935 ----------------------------------------------------------------------------- Trying gamma equal 2.26446260E-02 Gamma decreased to 1.51314782E-02 fvalues 109017.92 5550.6162 996259.38 996622.63 CGMAT cycle number = 5 fast hessian tabulation Weight matrix 3.2855875 Actual weight 8.2644625 is applied to the X-ray term function value 906067.94 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.024 0.019 Bond distances: others 962 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.920, B = -0.010 Babinet"s bulk solvent: scale = 0.167, B = 153.567 Partial structure 1: scale = 0.427, B = 30.568 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 = 0.1644 Free R factor = 0.1912 Overall figure of merit = 0.8940 ----------------------------------------------------------------------------- Trying gamma equal 1.51314782E-02 Gamma decreased to 8.30134377E-03 fvalues 108972.11 5476.9287 905848.38 906072.81 CGMAT cycle number = 6 fast hessian tabulation Weight matrix 3.2973082 Actual weight 8.2644625 is applied to the X-ray term function value 905808.75 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.024 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.011 Babinet"s bulk solvent: scale = 0.167, B = 153.567 Partial structure 1: scale = 0.427, B = 30.578 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 = 0.1643 Free R factor = 0.1910 Overall figure of merit = 0.8943 ----------------------------------------------------------------------------- Trying gamma equal 8.30134377E-03 Gamma decreased to 2.09213095E-03 fvalues 108953.75 5363.7515 905650.25 905807.94 CGMAT cycle number = 7 fast hessian tabulation Weight matrix 3.3121138 Actual weight 8.2644625 is applied to the X-ray term function value 905600.69 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.011 Babinet"s bulk solvent: scale = 0.165, B = 153.566 Partial structure 1: scale = 0.428, B = 30.496 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 = 0.1641 Free R factor = 0.1910 Overall figure of merit = 0.8945 ----------------------------------------------------------------------------- Trying gamma equal 2.09213095E-03 Gamma decreased to 0.0000000 fvalues 108936.92 5302.3296 905490.06 905607.44 CGMAT cycle number = 8 fast hessian tabulation Weight matrix 3.3133535 Actual weight 8.2644625 is applied to the X-ray term function value 905473.69 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.011 Babinet"s bulk solvent: scale = 0.165, B = 153.566 Partial structure 1: scale = 0.428, B = 30.458 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 = 0.1640 Free R factor = 0.1911 Overall figure of merit = 0.8945 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 2.56579034E-02 Gamma decreased to 2.05263235E-02 fvalues 108926.01 5263.0693 905376.75 905478.00 CGMAT cycle number = 9 fast hessian tabulation Weight matrix 3.3147881 Actual weight 8.2644625 is applied to the X-ray term function value 905384.75 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.011 Babinet"s bulk solvent: scale = 0.165, B = 153.565 Partial structure 1: scale = 0.428, B = 30.422 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 = 0.1639 Free R factor = 0.1911 Overall figure of merit = 0.8946 ----------------------------------------------------------------------------- Trying gamma equal 2.05263235E-02 Gamma decreased to 1.58612505E-02 fvalues 108918.50 5232.9355 905325.50 905385.81 CGMAT cycle number = 10 fast hessian tabulation Weight matrix 3.3256834 Actual weight 8.2644625 is applied to the X-ray term function value 905341.69 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.012 Babinet"s bulk solvent: scale = 0.164, B = 153.565 Partial structure 1: scale = 0.428, B = 30.421 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 = 0.1639 Free R factor = 0.1911 Overall figure of merit = 0.8947 ----------------------------------------------------------------------------- Trying gamma equal 1.58612505E-02 Gamma decreased to 1.16202747E-02 fvalues 108914.98 5215.8599 905286.19 905339.63 CGMAT cycle number = 11 fast hessian tabulation Weight matrix 3.3256543 Actual weight 8.2644625 is applied to the X-ray term function value 905287.31 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.013 Babinet"s bulk solvent: scale = 0.164, B = 153.562 Partial structure 1: scale = 0.428, B = 30.179 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 = 0.1638 Free R factor = 0.1911 Overall figure of merit = 0.8948 ----------------------------------------------------------------------------- Trying gamma equal 1.16202747E-02 Gamma decreased to 7.76484236E-03 fvalues 108909.69 5209.3257 905260.25 905289.38 CGMAT cycle number = 12 fast hessian tabulation Weight matrix 3.3282366 Actual weight 8.2644625 is applied to the X-ray term function value 905267.38 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.015 Babinet"s bulk solvent: scale = 0.164, B = 153.562 Partial structure 1: scale = 0.428, B = 30.178 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 = 0.1638 Free R factor = 0.1913 Overall figure of merit = 0.8948 ----------------------------------------------------------------------------- Trying gamma equal 7.76484236E-03 Gamma decreased to 4.25990392E-03 fvalues 108907.60 5202.8374 905241.50 905265.63 CGMAT cycle number = 13 fast hessian tabulation Weight matrix 3.3265927 Actual weight 8.2644625 is applied to the X-ray term function value 905278.25 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.016 Babinet"s bulk solvent: scale = 0.164, B = 153.562 Partial structure 1: scale = 0.428, B = 30.160 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 = 0.1638 Free R factor = 0.1913 Overall figure of merit = 0.8948 ----------------------------------------------------------------------------- Trying gamma equal 4.25990392E-03 Gamma decreased to 1.07359642E-03 fvalues 108908.56 5206.0088 905269.94 905276.75 CGMAT cycle number = 14 fast hessian tabulation Weight matrix 3.3242385 Actual weight 8.2644625 is applied to the X-ray term function value 905289.81 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.015 Babinet"s bulk solvent: scale = 0.164, B = 153.562 Partial structure 1: scale = 0.427, B = 30.195 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 = 0.1638 Free R factor = 0.1914 Overall figure of merit = 0.8948 ----------------------------------------------------------------------------- Trying gamma equal 1.07359642E-03 Gamma decreased to 0.0000000 fvalues 108910.59 5202.6812 905295.06 905290.19 fvalues 108910.59 5202.6812 905293.38 905290.19 CGMAT cycle number = 15 fast hessian tabulation Weight matrix 3.3231118 Actual weight 8.2644625 is applied to the X-ray term function value 905311.19 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.015 Babinet"s bulk solvent: scale = 0.164, B = 153.563 Partial structure 1: scale = 0.428, B = 30.293 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 = 0.1638 Free R factor = 0.1914 Overall figure of merit = 0.8947 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 1.31665589E-02 Gamma decreased to 1.05332471E-02 fvalues 108913.42 5200.1509 905292.94 905311.06 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\r41.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= 0.9001E+06 GEOM= 5200. TOTAL= 0.9053E+06 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.003 0.020 Bond angles : refined atoms 1408 2.208 1.903 Bond angles : others 2180 1.017 3.007 Torsion angles, period 1. refined 132 6.422 5.000 Torsion angles, period 2. refined 51 36.434 22.745 Torsion angles, period 3. refined 169 12.321 15.000 Torsion angles, period 3. others 8 3.975 15.000 Torsion angles, period 4. refined 12 24.316 15.000 Chiral centres: refined atoms 146 0.145 0.200 Planar groups: refined atoms 1225 0.012 0.020 Planar groups: others 277 0.001 0.020 VDW repulsions: refined_atoms 311 0.267 0.200 VDW repulsions.others 896 0.176 0.200 VDW; torsion: refined_atoms 521 0.187 0.200 VDW; torsion.others 580 0.088 0.200 HBOND: refined_atoms 15 0.154 0.200 Metal-ion: refined_atoms 4 0.121 0.200 VDW repulsions: symmetry: refined_atoms 18 0.254 0.200 VDW repulsions: symmetry: others 24 0.151 0.200 HBOND: symmetry: refined_atoms 2 0.106 0.200 M. chain bond B values: refined atoms 519 1.247 0.897 M. chain bond B values: others 518 1.212 0.894 M. chain angle B values: refined atoms 648 1.788 1.348 M. chain angle B values: others 649 1.791 1.351 S. chain bond B values: refined atoms 518 2.431 1.124 S. chain bond B values: others 518 2.431 1.123 S. chain angle B values: refined atoms 758 3.265 1.606 S. chain angle B values: others 758 3.260 1.605 Long range B values: refined atoms 1302 4.233 8.040 Long range B values: others 1262 4.127 7.750 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.015 Babinet"s bulk solvent: scale = 0.164, B = 153.564 Partial structure 1: scale = 0.428, B = 30.324 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 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 619.4 598.8 0.21 0.30 14 397.9 435.8 0.19 0.24 0.040 535 100.00 518.0 545.6 0.19 0.26 34 547.4 592.5 0.20 0.33 0.067 672 100.00 577.2 550.7 0.17 0.22 32 528.5 532.5 0.19 0.23 0.094 779 99.75 471.9 441.6 0.18 0.23 31 501.7 440.8 0.21 0.23 0.121 879 100.00 344.0 338.0 0.19 0.23 43 325.0 312.2 0.18 0.23 0.148 958 100.00 283.0 290.4 0.18 0.20 42 263.3 259.8 0.19 0.23 0.174 1040 100.00 263.0 265.1 0.16 0.18 38 280.2 295.3 0.15 0.18 0.201 1096 100.00 243.5 236.6 0.15 0.17 65 234.1 234.1 0.18 0.19 0.228 1185 100.00 220.0 216.2 0.15 0.16 56 231.7 219.0 0.15 0.17 0.255 1205 100.00 189.8 185.3 0.15 0.16 82 186.0 186.9 0.20 0.22 0.281 1298 100.00 162.7 159.6 0.16 0.16 59 156.8 155.2 0.20 0.21 0.308 1337 100.00 140.8 140.0 0.16 0.16 76 137.1 136.6 0.20 0.20 0.335 1403 100.00 126.4 124.0 0.16 0.15 88 120.4 118.2 0.23 0.22 0.362 1434 100.00 118.8 114.3 0.15 0.14 74 115.5 106.4 0.19 0.19 0.388 1507 100.00 110.7 107.2 0.15 0.14 76 106.0 102.8 0.19 0.17 0.415 1532 100.00 99.5 95.7 0.15 0.14 97 99.7 91.8 0.19 0.18 0.442 1579 100.00 93.7 90.0 0.15 0.13 92 95.0 88.8 0.17 0.17 0.469 1633 100.00 87.6 84.1 0.15 0.13 109 87.7 83.9 0.20 0.18 0.495 1576 93.50 76.0 74.3 0.16 0.14 79 79.2 75.3 0.21 0.18 0.522 1250 72.50 72.9 71.6 0.15 0.13 63 69.7 64.8 0.21 0.18 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.908 140 0.831 319 0.874 0.967 0.0405 376 0.925 159 0.823 535 0.895 0.978 0.0672 518 0.939 154 0.834 672 0.915 0.986 0.0940 623 0.925 156 0.855 779 0.911 0.992 0.1208 716 0.876 163 0.776 879 0.858 0.993 0.1475 800 0.901 158 0.767 958 0.879 0.967 0.1743 883 0.928 157 0.809 1040 0.910 0.958 0.2010 934 0.927 162 0.847 1096 0.915 0.978 0.2278 1022 0.934 163 0.864 1185 0.924 0.987 0.2546 1048 0.910 157 0.850 1205 0.902 0.981 0.2813 1136 0.883 162 0.803 1298 0.873 0.969 0.3081 1176 0.894 161 0.799 1337 0.883 0.963 0.3349 1243 0.894 160 0.821 1403 0.886 0.970 0.3616 1269 0.886 165 0.748 1434 0.870 0.984 0.3884 1347 0.905 160 0.878 1507 0.902 0.991 0.4151 1380 0.914 152 0.814 1532 0.904 0.989 0.4419 1421 0.919 158 0.862 1579 0.914 0.998 0.4687 1477 0.907 156 0.859 1633 0.902 0.990 0.4954 1447 0.885 131 0.778 1578 0.876 0.974 0.5222 1161 0.898 87 0.835 1248 0.894 0.968 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.1637 Free R factor = 0.1914 Overall weighted R factor = 0.1738 Free weighted R factor = 0.2041 Overall weighted R2 factor = 0.2373 Free weighted R2 factor = 0.2714 Overall correlation coefficient = 0.9605 Free correlation coefficient = 0.9472 Cruickshanks DPI for coordinate error= 0.0562 DPI based on free R factor = 0.0590 Overall figure of merit = 0.8947 ML based su of positional parameters = 0.0328 ML based su of thermal parameters = 0.7753 ----------------------------------------------------------------------------- Time in seconds: CPU = 0.00 Elapsed = 71.00 **** 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: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.1805 0.2008 0.881 111167. 6077.7 0.0219 1.149 2.146 1.094 0.133 1 0.1722 0.1957 0.887 110061. 6033.8 0.0220 1.137 2.140 1.094 0.136 2 0.1664 0.1924 0.892 109233. 6000.6 0.0237 1.221 2.218 1.143 0.143 3 0.1648 0.1915 0.893 109018. 5992.1 0.0243 1.255 2.272 1.175 0.147 4 0.1644 0.1912 0.894 108972. 5989.5 0.0241 1.239 2.264 1.171 0.147 5 0.1643 0.1910 0.894 108954. 5987.9 0.0235 1.210 2.241 1.158 0.146 6 0.1641 0.1910 0.894 108936. 5986.9 0.0232 1.193 2.227 1.150 0.145 7 0.1640 0.1911 0.895 108925. 5986.9 0.0230 1.184 2.219 1.146 0.145 8 0.1639 0.1911 0.895 108918. 5986.8 0.0229 1.178 2.214 1.143 0.145 9 0.1639 0.1911 0.895 108915. 5986.7 0.0229 1.175 2.211 1.142 0.145 10 0.1638 0.1911 0.895 108909. 5986.9 0.0229 1.174 2.209 1.141 0.145 11 0.1638 0.1913 0.895 108908. 5986.8 0.0228 1.173 2.208 1.141 0.145 12 0.1638 0.1913 0.895 108909. 5987.2 0.0228 1.173 2.208 1.141 0.145 13 0.1638 0.1914 0.895 108911. 5987.5 0.0228 1.173 2.208 1.142 0.145 14 0.1638 0.1914 0.895 108913. 5987.6 0.0228 1.173 2.208 1.141 0.145 15 0.1637 0.1914 0.895 108914. 5987.9 0.0228 1.173 2.208 1.141 0.145 $$ $TEXT:Result: $$ Final results $$ Initial Final R factor 0.1805 0.1637 R free 0.2008 0.1914 Rms BondLength 0.0219 0.0228 Rms BondAngle 2.1456 2.2081 Rms ChirVolume 0.1332 0.1453 $$
Refmac_5.7.0032: End of Refmac_5.7.0032 Times: User: 0.0s System: 0.0s Elapsed: 1:23
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CCP4i: Writing final coordinates (XYZOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r41.pdb
CCP4i: Writing final phases (HKLOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r41.mtz
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