Summary:
Initial | After 10 cycles | |
---|---|---|
R factor | 0.2611 | 0.2609 |
Rfree | 0.2790 | 0.2776 |
RMSD Bond Length | 0.0240 | 0.0223 |
RMSD Bond Angle | 2.340 | 2.178 |
RMSD Chiral Centre | 0.148 | 0.138 |
Result:
Initial | Final | |
---|---|---|
R factor | 0.2611 | 0.2609 |
R free | 0.2790 | 0.2776 |
Rms BondLength | 0.0240 | 0.0223 |
Rms BondAngle | 2.3404 | 2.1780 |
Rms ChirVolume | 0.1478 | 0.1377 |
Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Rfactor analysis, stats vs cycle |
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############################################################### ############################################################### ############################################################### ### CCP4 6.3: Refmac_5.7.0032 version 5.7.0032 : 05/09/12## ############################################################### User: Administrator Run date: 10/ 5/2013 Run time: 19:22:59 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\r21.pdb Output coordinate file. Logical name - XYZOUT actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r211.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\r211.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\r21.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 = 1.993 ideal_dist= 2.031 ch:AA res: 6 CYS at:SG .->AA res: 127 CYS at:SG . WARNING : link:SS is found dist = 2.067 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 = 2.042 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 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 1.6119665 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 53.3 Norm of Geom. positional gradient 67.2 Norm of X_ray B-factor gradient 236. Norm of Geom. B-factor gradient 188. Product of X_ray and Geom posit. gradients -0.145E+08 Cosine of angle between them -0.736 Product of X_ray and Geom B-fact gradients -0.662E+08 Cosine of angle between them -0.813 Residuals: XRAY= 0.1172E+07 GEOM= 6986. TOTAL= 0.1179E+07 function value 1178874.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.024 0.019 Bond distances: others 877 0.000 0.020 Bond angles : refined atoms 1322 2.340 1.903 Bond angles : others 1990 4.021 3.008 Torsion angles, period 1. refined 127 6.168 5.000 Torsion angles, period 2. refined 43 38.274 24.419 Torsion angles, period 3. refined 148 14.012 15.000 Torsion angles, period 3. others 8 45.884 15.000 Torsion angles, period 4. refined 6 16.665 15.000 Chiral centres: refined atoms 142 0.148 0.200 Planar groups: refined atoms 1154 0.012 0.020 Planar groups: others 242 0.023 0.020 VDW repulsions: refined_atoms 203 0.234 0.200 VDW repulsions.others 751 0.236 0.200 VDW; torsion: refined_atoms 498 0.186 0.200 VDW; torsion.others 489 0.113 0.200 HBOND: refined_atoms 12 0.132 0.200 HBOND.others 1 0.004 0.200 VDW repulsions: symmetry: refined_atoms 3 0.059 0.200 VDW repulsions: symmetry: others 9 0.134 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 7.246 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.957, B = -0.005 Babinet"s bulk solvent: scale = 0.185, B = 116.456 Partial structure 1: scale = 0.450, B = 17.442 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 333.5 314.0 0.26 0.36 14 218.2 224.3 0.24 0.30 0.040 535 100.00 349.4 368.2 0.24 0.33 34 370.8 406.2 0.28 0.41 0.067 672 100.00 427.0 396.2 0.24 0.32 32 364.5 339.0 0.25 0.34 0.094 779 99.75 362.2 319.3 0.28 0.33 31 372.7 342.7 0.24 0.29 0.121 879 100.00 268.9 258.8 0.30 0.35 43 275.6 262.6 0.30 0.37 0.148 958 100.00 226.8 231.3 0.29 0.34 42 204.6 212.2 0.33 0.37 0.174 1040 100.00 214.3 210.4 0.27 0.30 38 226.5 226.7 0.28 0.33 0.201 1096 100.00 199.1 187.3 0.28 0.31 65 190.1 184.5 0.33 0.35 0.228 1185 100.00 182.1 174.1 0.26 0.28 56 198.5 191.3 0.26 0.29 0.255 1205 100.00 158.4 152.5 0.26 0.27 82 165.4 161.9 0.27 0.28 0.281 1298 100.00 136.6 129.7 0.26 0.27 59 135.2 132.0 0.30 0.31 0.308 1337 100.00 118.8 114.7 0.25 0.25 76 121.2 112.8 0.29 0.28 0.335 1403 100.00 107.5 101.8 0.25 0.24 88 101.1 99.5 0.29 0.27 0.362 1434 100.00 100.9 94.4 0.25 0.23 74 104.9 92.2 0.25 0.24 0.388 1507 100.00 95.0 88.7 0.24 0.22 76 91.0 84.6 0.25 0.23 0.415 1532 100.00 86.0 81.0 0.24 0.22 97 83.9 73.3 0.29 0.27 0.442 1579 100.00 80.9 76.3 0.22 0.21 92 82.2 75.1 0.27 0.25 0.469 1633 100.00 76.0 69.8 0.24 0.22 109 71.0 68.7 0.27 0.24 0.495 1576 93.50 66.9 62.9 0.25 0.22 79 72.2 67.4 0.28 0.25 0.522 1250 72.50 64.9 62.1 0.24 0.21 63 64.8 61.1 0.27 0.24 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.846 140 0.748 319 0.803 0.941 0.0405 376 0.866 159 0.748 535 0.831 0.948 0.0672 518 0.887 154 0.765 672 0.859 0.954 0.0940 623 0.850 156 0.778 779 0.836 0.959 0.1208 716 0.775 163 0.678 879 0.757 0.958 0.1475 800 0.788 158 0.647 958 0.765 0.928 0.1743 883 0.814 157 0.681 1040 0.794 0.919 0.2010 934 0.809 162 0.679 1096 0.790 0.944 0.2278 1022 0.838 163 0.709 1185 0.821 0.957 0.2546 1048 0.830 157 0.765 1205 0.822 0.949 0.2813 1136 0.799 162 0.674 1298 0.783 0.933 0.3081 1176 0.796 161 0.655 1337 0.779 0.931 0.3349 1243 0.819 160 0.747 1403 0.810 0.955 0.3616 1269 0.815 165 0.678 1434 0.799 0.958 0.3884 1347 0.822 160 0.770 1507 0.816 0.967 0.4151 1380 0.831 152 0.749 1532 0.823 0.966 0.4419 1421 0.852 158 0.771 1579 0.844 0.975 0.4687 1477 0.820 156 0.756 1633 0.814 0.974 0.4954 1447 0.791 131 0.646 1578 0.779 0.958 0.5222 1161 0.808 87 0.728 1248 0.802 0.946 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.2611 Free R factor = 0.2790 Overall weighted R factor = 0.2761 Free weighted R factor = 0.2984 Overall weighted R2 factor = 0.3648 Free weighted R2 factor = 0.4056 Overall correlation coefficient = 0.9031 Free correlation coefficient = 0.8860 Cruickshanks DPI for coordinate error= 0.0810 DPI based on free R factor = 0.0792 Overall figure of merit = 0.8056 ML based su of positional parameters = 0.0495 ML based su of thermal parameters = 1.1577 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 5.00000007E-02 Gamma decreased to 3.99999991E-02 fvalues 117188.84 6986.3701 1176406.9 1178874.8 CGMAT cycle number = 2 fast hessian tabulation Weight matrix 1.6271582 Actual weight 10.000000 is applied to the X-ray term function value 1176373.6 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.024 0.019 Bond distances: others 877 0.006 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.957, B = -0.058 Babinet"s bulk solvent: scale = 0.183, B = 116.455 Partial structure 1: scale = 0.450, B = 17.396 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 = 0.2606 Free R factor = 0.2787 Overall figure of merit = 0.8062 ----------------------------------------------------------------------------- Trying gamma equal 3.99999991E-02 Gamma decreased to 3.09090894E-02 fvalues 117143.86 4930.3154 1176161.4 1176368.9 CGMAT cycle number = 3 fast hessian tabulation Weight matrix 1.4839255 Actual weight 9.0909090 is applied to the X-ray term function value 1069693.8 ------------------------------------------------------------------------------- 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 = 0.957, B = -0.046 Babinet"s bulk solvent: scale = 0.183, B = 116.456 Partial structure 1: scale = 0.450, B = 17.496 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 = 0.2603 Free R factor = 0.2784 Overall figure of merit = 0.8066 ----------------------------------------------------------------------------- Trying gamma equal 3.09090894E-02 Gamma decreased to 2.26446260E-02 fvalues 117125.70 4917.8711 1069589.9 1069696.9 CGMAT cycle number = 4 fast hessian tabulation Weight matrix 1.3526835 Actual weight 8.2644625 is applied to the X-ray term function value 972770.38 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.023 0.019 Bond distances: others 877 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.957, B = -0.043 Babinet"s bulk solvent: scale = 0.184, B = 116.455 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 = 0.2605 Free R factor = 0.2780 Overall figure of merit = 0.8069 ----------------------------------------------------------------------------- Trying gamma equal 2.26446260E-02 Gamma decreased to 1.51314782E-02 fvalues 117132.52 4732.1309 972699.06 972769.44 CGMAT cycle number = 5 fast hessian tabulation Weight matrix 1.3546566 Actual weight 8.2644625 is applied to the X-ray term function value 972766.94 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.023 0.019 Bond distances: others 877 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.956, B = -0.046 Babinet"s bulk solvent: scale = 0.182, B = 116.453 Partial structure 1: scale = 0.449, B = 17.297 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 = 0.2607 Free R factor = 0.2778 Overall figure of merit = 0.8071 ----------------------------------------------------------------------------- Trying gamma equal 1.51314782E-02 Gamma decreased to 8.30134377E-03 fvalues 117161.14 4498.4736 972754.63 972772.31 CGMAT cycle number = 6 fast hessian tabulation Weight matrix 1.3576297 Actual weight 8.2644625 is applied to the X-ray term function value 972798.25 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.022 0.019 Bond distances: others 877 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.956, B = -0.042 Babinet"s bulk solvent: scale = 0.181, B = 116.451 Partial structure 1: scale = 0.449, B = 17.174 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 = 0.2608 Free R factor = 0.2776 Overall figure of merit = 0.8072 ----------------------------------------------------------------------------- Trying gamma equal 8.30134377E-03 Gamma decreased to 2.09213095E-03 fvalues 117171.19 4437.5645 972773.13 972794.44 CGMAT cycle number = 7 fast hessian tabulation Weight matrix 1.3571830 Actual weight 8.2644625 is applied to the X-ray term function value 972791.75 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.022 0.019 Bond distances: others 877 0.002 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.956, B = -0.047 Babinet"s bulk solvent: scale = 0.181, B = 116.451 Partial structure 1: scale = 0.449, B = 17.180 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 = 0.2609 Free R factor = 0.2776 Overall figure of merit = 0.8072 ----------------------------------------------------------------------------- Trying gamma equal 2.09213095E-03 Gamma decreased to 0.0000000 fvalues 117175.63 4397.1538 972793.63 972790.75 fvalues 117175.63 4397.1538 972785.38 972790.75 CGMAT cycle number = 8 fast hessian tabulation Weight matrix 1.3600143 Actual weight 8.2644625 is applied to the X-ray term function value 972799.94 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.022 0.019 Bond distances: others 877 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.956, B = -0.047 Babinet"s bulk solvent: scale = 0.180, B = 116.450 Partial structure 1: scale = 0.449, B = 17.153 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 = 0.2609 Free R factor = 0.2776 Overall figure of merit = 0.8072 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 2.56579034E-02 Gamma decreased to 2.05263235E-02 fvalues 117178.05 4386.0947 972789.69 972799.75 CGMAT cycle number = 9 fast hessian tabulation Weight matrix 1.3594744 Actual weight 8.2644625 is applied to the X-ray term function value 972820.00 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.022 0.019 Bond distances: others 877 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.956, B = -0.046 Babinet"s bulk solvent: scale = 0.180, B = 116.450 Partial structure 1: scale = 0.449, B = 17.131 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 = 0.2609 Free R factor = 0.2777 Overall figure of merit = 0.8072 ----------------------------------------------------------------------------- Trying gamma equal 2.05263235E-02 Gamma decreased to 1.58612505E-02 fvalues 117182.09 4373.1729 972811.50 972820.19 CGMAT cycle number = 10 fast hessian tabulation Weight matrix 1.3594893 Actual weight 8.2644625 is applied to the X-ray term function value 972842.13 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.022 0.019 Bond distances: others 877 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.956, B = -0.047 Babinet"s bulk solvent: scale = 0.180, B = 116.448 Partial structure 1: scale = 0.449, B = 17.032 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 = 0.2609 Free R factor = 0.2778 Overall figure of merit = 0.8072 ----------------------------------------------------------------------------- Trying gamma equal 1.58612505E-02 Gamma decreased to 1.16202747E-02 fvalues 117185.05 4365.6821 972834.00 972837.19 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\r211.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= 0.9685E+06 GEOM= 4361. TOTAL= 0.9729E+06 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 973 0.022 0.019 Bond distances: others 877 0.001 0.020 Bond angles : refined atoms 1322 2.178 1.903 Bond angles : others 1990 1.050 3.008 Torsion angles, period 1. refined 127 6.180 5.000 Torsion angles, period 2. refined 43 38.194 24.419 Torsion angles, period 3. refined 148 12.787 15.000 Torsion angles, period 3. others 8 14.811 15.000 Torsion angles, period 4. refined 6 22.601 15.000 Chiral centres: refined atoms 142 0.138 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 817 0.174 0.200 VDW; torsion: refined_atoms 495 0.185 0.200 VDW; torsion.others 528 0.091 0.200 HBOND: refined_atoms 14 0.122 0.200 VDW repulsions: symmetry: refined_atoms 3 0.061 0.200 VDW repulsions: symmetry: others 9 0.121 0.200 HBOND: symmetry: refined_atoms 1 0.189 0.200 M. chain bond B values: refined atoms 511 0.999 0.915 M. chain bond B values: others 510 0.979 0.914 M. chain angle B values: refined atoms 637 1.453 1.374 M. chain angle B values: others 638 1.452 1.375 S. chain bond B values: refined atoms 462 1.523 1.014 S. chain bond B values: others 463 1.521 1.014 S. chain angle B values: refined atoms 685 2.252 1.473 S. chain angle B values: others 685 2.252 1.473 Long range B values: refined atoms 1118 2.581 7.269 Long range B values: others 1119 2.580 7.275 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.956, B = -0.046 Babinet"s bulk solvent: scale = 0.179, B = 116.447 Partial structure 1: scale = 0.449, B = 16.993 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 595.6 561.3 0.26 0.36 14 382.5 395.8 0.26 0.32 0.040 535 100.00 498.0 524.0 0.24 0.32 34 526.3 577.3 0.28 0.42 0.067 672 100.00 555.0 514.9 0.24 0.32 32 508.1 473.4 0.25 0.33 0.094 779 99.75 453.7 400.8 0.28 0.33 31 482.3 442.4 0.24 0.28 0.121 879 100.00 330.7 319.3 0.30 0.35 43 312.5 300.0 0.29 0.37 0.148 958 100.00 272.1 277.0 0.30 0.34 42 253.2 262.7 0.33 0.37 0.174 1040 100.00 252.9 248.4 0.28 0.31 38 269.4 268.7 0.28 0.33 0.201 1096 100.00 234.1 220.2 0.28 0.30 65 225.1 217.3 0.34 0.36 0.228 1185 100.00 211.5 202.4 0.26 0.28 56 222.8 213.2 0.26 0.28 0.255 1205 100.00 182.5 176.0 0.26 0.27 82 178.8 174.8 0.26 0.28 0.281 1298 100.00 156.4 148.5 0.27 0.27 59 150.8 148.0 0.30 0.31 0.308 1337 100.00 135.4 130.8 0.25 0.25 76 131.8 122.6 0.29 0.29 0.335 1403 100.00 121.6 115.3 0.25 0.24 88 115.7 113.8 0.29 0.27 0.362 1434 100.00 114.2 106.6 0.25 0.23 74 111.1 96.9 0.25 0.24 0.388 1507 100.00 106.4 99.4 0.24 0.22 76 101.9 94.5 0.24 0.22 0.415 1532 100.00 95.7 90.2 0.23 0.22 97 95.9 84.5 0.29 0.26 0.442 1579 100.00 90.1 85.0 0.22 0.20 92 91.3 83.5 0.26 0.24 0.469 1633 100.00 84.2 77.5 0.23 0.22 109 84.3 82.1 0.27 0.24 0.495 1576 93.50 73.0 68.6 0.24 0.22 79 76.2 71.1 0.28 0.25 0.522 1250 72.50 70.1 67.0 0.24 0.21 63 67.1 63.4 0.27 0.23 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.847 140 0.750 319 0.805 0.941 0.0405 376 0.867 159 0.748 535 0.832 0.948 0.0672 518 0.889 154 0.766 672 0.861 0.954 0.0940 623 0.854 156 0.785 779 0.840 0.959 0.1208 716 0.782 163 0.684 879 0.764 0.958 0.1475 800 0.790 158 0.648 958 0.767 0.928 0.1743 883 0.812 157 0.680 1040 0.792 0.919 0.2010 934 0.805 162 0.671 1096 0.786 0.944 0.2278 1022 0.837 163 0.705 1185 0.819 0.957 0.2546 1048 0.829 157 0.770 1205 0.821 0.949 0.2813 1136 0.800 162 0.674 1298 0.784 0.933 0.3081 1176 0.796 161 0.656 1337 0.779 0.931 0.3349 1243 0.817 160 0.741 1403 0.809 0.955 0.3616 1269 0.809 165 0.667 1434 0.793 0.958 0.3884 1347 0.824 160 0.773 1507 0.819 0.967 0.4151 1380 0.838 152 0.756 1532 0.830 0.968 0.4419 1421 0.861 158 0.788 1579 0.854 0.980 0.4687 1477 0.821 156 0.757 1633 0.815 0.974 0.4954 1447 0.793 131 0.648 1578 0.781 0.958 0.5222 1161 0.813 87 0.742 1248 0.808 0.946 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.2609 Free R factor = 0.2776 Overall weighted R factor = 0.2760 Free weighted R factor = 0.2976 Overall weighted R2 factor = 0.3642 Free weighted R2 factor = 0.4065 Overall correlation coefficient = 0.9033 Free correlation coefficient = 0.8862 Cruickshanks DPI for coordinate error= 0.0810 DPI based on free R factor = 0.0788 Overall figure of merit = 0.8072 ML based su of positional parameters = 0.0490 ML based su of thermal parameters = 1.1441 ----------------------------------------------------------------------------- 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: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.2611 0.2790 0.806 117189. 6346.9 0.0240 1.191 2.340 1.170 0.148 1 0.2606 0.2787 0.806 117144. 6344.8 0.0241 1.198 2.316 1.157 0.147 2 0.2603 0.2784 0.807 117125. 6344.4 0.0243 1.205 2.307 1.152 0.148 3 0.2605 0.2780 0.807 117133. 6343.6 0.0235 1.165 2.265 1.129 0.145 4 0.2607 0.2778 0.807 117160. 6343.4 0.0226 1.116 2.213 1.102 0.140 5 0.2608 0.2776 0.807 117172. 6343.8 0.0224 1.107 2.197 1.094 0.139 6 0.2609 0.2776 0.807 117176. 6344.1 0.0223 1.104 2.188 1.090 0.138 7 0.2609 0.2776 0.807 117178. 6344.1 0.0223 1.104 2.185 1.089 0.138 8 0.2609 0.2777 0.807 117182. 6344.6 0.0223 1.103 2.182 1.088 0.138 9 0.2609 0.2778 0.807 117186. 6344.7 0.0223 1.103 2.179 1.088 0.138 10 0.2609 0.2776 0.807 117188. 6344.8 0.0223 1.103 2.178 1.088 0.138 $$ $TEXT:Result: $$ Final results $$ Initial Final R factor 0.2611 0.2609 R free 0.2790 0.2776 Rms BondLength 0.0240 0.0223 Rms BondAngle 2.3404 2.1780 Rms ChirVolume 0.1478 0.1377 $$
Refmac_5.7.0032: End of Refmac_5.7.0032 Times: User: 0.0s System: 0.0s Elapsed: 0:54
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CCP4i: Writing final coordinates (XYZOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r211.pdb
CCP4i: Writing final phases (HKLOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r211.mtz
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