Summary:
Initial | After 25 cycles | |
---|---|---|
R factor | 0.1807 | 0.1590 |
Rfree | 0.2006 | 0.1848 |
RMSD Bond Length | 0.0 | 0.0207 |
RMSD Bond Angle | 0.0 | 2.098 |
RMSD Chiral Centre | 0.0 | 0.141 |
Result:
Initial | Final | |
---|---|---|
R factor | 0.1807 | 0.1590 |
R free | 0.2006 | 0.1848 |
Rms BondLength | 0.0219 | 0.0207 |
Rms BondAngle | 2.1456 | 2.0978 |
Rms ChirVolume | 0.1332 | 0.1414 |
The following tables were found in the logfile: Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 10. Rfactor analysis, F distribution v resln Cycle 10. 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 Cycle 26. Rfactor analysis, F distribution v resln Cycle 26. Fom(<cos(DelPhi)>-acentric, centric, overall v resln |
Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 10. Rfactor analysis, F distribution v resln Cycle 10. 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 Cycle 26. Rfactor analysis, F distribution v resln Cycle 26. 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: 20:39:14 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--- refi tlsc 10 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\r42.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\r42.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 Data line--- TLS chain A Data line--- RANGE 'A 1.' 'A 129.' ALL ###### TLS Group Definitions ###### Group: 1: No. of pieces: 1 Chain: A Span: 1 129 Calculating TLS origin of group 1 from centroid of group. TLS origin for group 1 0.82065988 20.340693 8.8515692 Initial TLS parameters TLS group 1: chain A T tensor ( 1) = 0.000 0.000 0.000 0.000 0.000 0.000 L tensor ( 1) = 0.000 0.000 0.000 0.000 0.000 0.000 S tensor ( 1) = 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 ***TLS refinement cycle*** 1 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.921, B = -0.175 Babinet"s bulk solvent: scale = 0.180, B = 153.590 Partial structure 1: scale = 0.426, B = 31.826 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 346.7 335.5 0.22 0.30 14 226.8 241.4 0.20 0.25 0.040 535 100.00 363.1 383.5 0.20 0.27 34 385.4 421.8 0.21 0.33 0.067 672 100.00 443.8 421.3 0.18 0.24 32 378.9 380.2 0.18 0.23 0.094 779 99.75 376.4 350.6 0.19 0.23 31 387.4 347.6 0.20 0.22 0.121 879 100.00 279.5 273.7 0.19 0.24 43 286.5 278.0 0.18 0.24 0.148 958 100.00 235.7 242.4 0.19 0.22 42 212.6 211.6 0.22 0.26 0.174 1040 100.00 222.7 223.6 0.17 0.19 38 235.4 248.0 0.15 0.17 0.201 1096 100.00 207.0 199.6 0.17 0.18 65 197.6 195.7 0.19 0.21 0.228 1185 100.00 189.2 185.0 0.16 0.18 56 206.3 196.7 0.16 0.17 0.255 1205 100.00 164.6 159.1 0.17 0.18 82 171.9 170.9 0.21 0.22 0.281 1298 100.00 142.0 138.2 0.18 0.18 59 140.5 139.1 0.20 0.21 0.308 1337 100.00 123.5 122.1 0.18 0.18 76 126.0 122.7 0.22 0.22 0.335 1403 100.00 111.7 109.0 0.18 0.17 88 105.0 104.3 0.24 0.23 0.362 1434 100.00 104.9 100.1 0.17 0.16 74 109.0 100.3 0.20 0.19 0.388 1507 100.00 98.7 95.3 0.17 0.16 76 94.6 93.4 0.22 0.20 0.415 1532 100.00 89.4 86.0 0.17 0.16 97 87.2 80.1 0.21 0.19 0.442 1579 100.00 84.1 80.6 0.17 0.16 92 85.5 80.2 0.20 0.20 0.469 1633 100.00 79.0 75.4 0.17 0.16 109 73.8 72.0 0.23 0.20 0.495 1576 93.50 69.6 67.9 0.19 0.17 79 75.0 72.0 0.23 0.19 0.522 1250 72.50 67.5 66.1 0.18 0.16 63 67.4 63.0 0.22 0.20 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.910 140 0.839 319 0.879 0.963 0.0405 376 0.925 159 0.828 535 0.896 0.975 0.0672 518 0.938 154 0.827 672 0.913 0.984 0.0940 623 0.924 156 0.856 779 0.911 0.991 0.1208 716 0.873 163 0.771 879 0.854 0.992 0.1475 800 0.894 158 0.761 958 0.872 0.963 0.1743 883 0.920 157 0.800 1040 0.902 0.953 0.2010 934 0.923 162 0.860 1096 0.913 0.977 0.2278 1022 0.925 163 0.852 1185 0.915 0.987 0.2546 1048 0.904 157 0.829 1205 0.894 0.981 0.2813 1136 0.883 162 0.800 1298 0.873 0.969 0.3081 1176 0.884 161 0.774 1337 0.871 0.964 0.3349 1243 0.879 160 0.811 1403 0.871 0.970 0.3616 1269 0.884 165 0.745 1434 0.868 0.982 0.3884 1347 0.882 160 0.844 1507 0.878 0.984 0.4151 1380 0.890 152 0.779 1532 0.879 0.981 0.4419 1421 0.890 158 0.822 1579 0.883 0.987 0.4687 1477 0.883 156 0.832 1633 0.878 0.982 0.4954 1447 0.858 131 0.741 1578 0.849 0.966 0.5222 1161 0.879 87 0.805 1248 0.874 0.963 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.1807 Free R factor = 0.2006 Overall weighted R factor = 0.1920 Free weighted R factor = 0.2151 Overall weighted R2 factor = 0.2558 Free weighted R2 factor = 0.2848 Overall correlation coefficient = 0.9544 Free correlation coefficient = 0.9435 Cruickshanks DPI for coordinate error= 0.0557 DPI based on free R factor = 0.0619 Overall figure of merit = 0.8814 ML based su of positional parameters = 0.0366 ML based su of thermal parameters = 1.7499 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.001 0.003 0.005 -0.001 -0.000 -0.000 L tensor ( 1) = 0.120 0.115 0.075 0.079 0.019 0.008 S tensor ( 1) = 0.014 -0.005 -0.003 -0.006 -0.019 -0.006 -0.000 -0.007 ***TLS refinement cycle*** 2 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.923, B = -0.630 Babinet"s bulk solvent: scale = 0.182, B = 153.597 Partial structure 1: scale = 0.426, B = 32.476 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 = 0.1787 Free R factor = 0.1980 Overall figure of merit = 0.8844 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.002 0.005 0.008 -0.002 -0.000 -0.001 L tensor ( 1) = 0.197 0.188 0.121 0.130 0.029 0.012 S tensor ( 1) = 0.023 -0.008 -0.004 -0.010 -0.030 -0.011 -0.001 -0.010 ***TLS refinement cycle*** 3 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.924, B = -0.864 Babinet"s bulk solvent: scale = 0.184, B = 153.593 Partial structure 1: scale = 0.426, B = 32.483 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 = 0.1778 Free R factor = 0.1969 Overall figure of merit = 0.8856 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.002 0.006 0.010 -0.002 -0.000 -0.001 L tensor ( 1) = 0.249 0.237 0.151 0.166 0.035 0.013 S tensor ( 1) = 0.028 -0.011 -0.005 -0.013 -0.038 -0.013 -0.001 -0.013 ***TLS refinement cycle*** 4 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.925, B = -0.994 Babinet"s bulk solvent: scale = 0.185, B = 153.588 Partial structure 1: scale = 0.426, B = 32.518 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 = 0.1774 Free R factor = 0.1964 Overall figure of merit = 0.8861 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.003 0.007 0.011 -0.003 -0.000 -0.002 L tensor ( 1) = 0.283 0.270 0.171 0.191 0.038 0.013 S tensor ( 1) = 0.032 -0.012 -0.005 -0.015 -0.043 -0.015 -0.001 -0.014 ***TLS refinement cycle*** 5 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.925, B = -1.094 Babinet"s bulk solvent: scale = 0.185, B = 153.583 Partial structure 1: scale = 0.426, B = 32.583 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 = 0.1771 Free R factor = 0.1961 Overall figure of merit = 0.8864 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.003 0.008 0.012 -0.003 -0.000 -0.002 L tensor ( 1) = 0.307 0.294 0.183 0.209 0.040 0.013 S tensor ( 1) = 0.035 -0.014 -0.006 -0.016 -0.046 -0.017 -0.001 -0.015 ***TLS refinement cycle*** 6 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.926, B = -1.172 Babinet"s bulk solvent: scale = 0.186, B = 153.578 Partial structure 1: scale = 0.426, B = 32.647 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 = 0.1770 Free R factor = 0.1959 Overall figure of merit = 0.8867 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.003 0.008 0.013 -0.004 -0.000 -0.001 L tensor ( 1) = 0.324 0.311 0.192 0.222 0.041 0.012 S tensor ( 1) = 0.037 -0.014 -0.006 -0.017 -0.049 -0.018 -0.001 -0.016 ***TLS refinement cycle*** 7 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.926, B = -1.231 Babinet"s bulk solvent: scale = 0.186, B = 153.573 Partial structure 1: scale = 0.426, B = 32.717 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 = 0.1769 Free R factor = 0.1957 Overall figure of merit = 0.8869 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.004 0.009 0.013 -0.004 -0.001 -0.001 L tensor ( 1) = 0.336 0.323 0.198 0.232 0.042 0.011 S tensor ( 1) = 0.038 -0.015 -0.006 -0.018 -0.050 -0.018 -0.001 -0.017 ***TLS refinement cycle*** 8 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.926, B = -1.277 Babinet"s bulk solvent: scale = 0.187, B = 153.568 Partial structure 1: scale = 0.426, B = 32.808 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 = 0.1768 Free R factor = 0.1956 Overall figure of merit = 0.8870 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.004 0.010 0.014 -0.004 -0.001 -0.001 L tensor ( 1) = 0.345 0.332 0.202 0.239 0.042 0.010 S tensor ( 1) = 0.039 -0.015 -0.006 -0.018 -0.051 -0.019 -0.000 -0.017 ***TLS refinement cycle*** 9 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.926, B = -1.311 Babinet"s bulk solvent: scale = 0.187, B = 153.561 Partial structure 1: scale = 0.426, B = 32.840 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 = 0.1768 Free R factor = 0.1954 Overall figure of merit = 0.8871 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.004 0.010 0.014 -0.004 -0.001 -0.001 L tensor ( 1) = 0.351 0.339 0.205 0.245 0.042 0.009 S tensor ( 1) = 0.040 -0.016 -0.006 -0.019 -0.052 -0.019 -0.000 -0.017 ***TLS refinement cycle*** 10 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.927, B = -1.338 Babinet"s bulk solvent: scale = 0.187, B = 153.554 Partial structure 1: scale = 0.426, B = 32.850 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 10. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 10. v. resln :N:1,6,7,11,12: :Cycle 10. and v. resln :N:1,4,5,9,10: :Cycle 10. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 614.2 594.9 0.22 0.30 14 394.5 420.1 0.20 0.25 0.040 535 100.00 513.7 542.3 0.20 0.27 34 542.8 591.5 0.20 0.32 0.067 672 100.00 572.4 544.0 0.18 0.23 32 524.1 525.8 0.18 0.24 0.094 779 99.75 468.0 436.3 0.19 0.23 31 497.5 447.5 0.21 0.23 0.121 879 100.00 341.1 334.2 0.19 0.23 43 322.3 313.3 0.18 0.23 0.148 958 100.00 280.6 288.2 0.19 0.22 42 261.1 258.5 0.21 0.24 0.174 1040 100.00 260.8 262.1 0.17 0.19 38 277.9 292.7 0.14 0.17 0.201 1096 100.00 241.4 233.0 0.16 0.18 65 232.1 229.1 0.19 0.21 0.228 1185 100.00 218.2 213.1 0.16 0.17 56 229.8 218.5 0.15 0.16 0.255 1205 100.00 188.2 181.5 0.16 0.17 82 184.4 182.2 0.20 0.21 0.281 1298 100.00 161.3 157.3 0.17 0.17 59 155.5 154.7 0.20 0.20 0.308 1337 100.00 139.6 138.7 0.18 0.17 76 136.0 131.5 0.20 0.21 0.335 1403 100.00 125.4 122.4 0.17 0.17 88 119.4 119.0 0.22 0.22 0.362 1434 100.00 117.8 112.6 0.17 0.16 74 114.6 107.0 0.19 0.18 0.388 1507 100.00 109.8 106.0 0.17 0.16 76 105.1 105.9 0.22 0.20 0.415 1532 100.00 98.7 95.1 0.16 0.15 97 98.9 91.0 0.20 0.19 0.442 1579 100.00 92.9 89.2 0.17 0.15 92 94.2 88.7 0.20 0.19 0.469 1633 100.00 86.9 83.2 0.17 0.15 109 86.9 84.6 0.22 0.20 0.495 1576 93.50 75.3 73.8 0.18 0.16 79 78.6 76.6 0.22 0.18 0.522 1250 72.50 72.3 71.2 0.17 0.15 63 69.2 63.2 0.22 0.20 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 10. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 10. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.912 140 0.841 319 0.881 0.963 0.0405 376 0.926 159 0.828 535 0.897 0.975 0.0672 518 0.938 154 0.827 672 0.913 0.984 0.0940 623 0.924 156 0.854 779 0.910 0.991 0.1208 716 0.870 163 0.780 879 0.854 0.992 0.1475 800 0.893 158 0.761 958 0.871 0.963 0.1743 883 0.921 157 0.800 1040 0.903 0.953 0.2010 934 0.926 162 0.864 1096 0.917 0.977 0.2278 1022 0.929 163 0.862 1185 0.920 0.987 0.2546 1048 0.909 157 0.823 1205 0.898 0.981 0.2813 1136 0.891 162 0.813 1298 0.881 0.969 0.3081 1176 0.893 161 0.787 1337 0.880 0.964 0.3349 1243 0.893 160 0.830 1403 0.885 0.970 0.3616 1269 0.897 165 0.760 1434 0.881 0.982 0.3884 1347 0.892 160 0.846 1507 0.887 0.984 0.4151 1380 0.898 152 0.794 1532 0.887 0.981 0.4419 1421 0.896 158 0.820 1579 0.888 0.987 0.4687 1477 0.890 156 0.834 1633 0.885 0.982 0.4954 1447 0.868 131 0.746 1578 0.858 0.966 0.5222 1161 0.879 87 0.823 1248 0.875 0.963 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.1767 Free R factor = 0.1954 Overall weighted R factor = 0.1876 Free weighted R factor = 0.2094 Overall weighted R2 factor = 0.2515 Free weighted R2 factor = 0.2783 Overall correlation coefficient = 0.9559 Free correlation coefficient = 0.9459 Cruickshanks DPI for coordinate error= 0.0545 DPI based on free R factor = 0.0603 Overall figure of merit = 0.8872 ML based su of positional parameters = 0.0354 ML based su of thermal parameters = 1.6608 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.004 0.010 0.014 -0.005 -0.001 -0.001 L tensor ( 1) = 0.356 0.344 0.207 0.249 0.042 0.009 S tensor ( 1) = 0.041 -0.016 -0.006 -0.019 -0.053 -0.020 -0.000 -0.017 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 3.4578958 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 100. Norm of Geom. positional gradient 69.1 Norm of X_ray B-factor gradient 257. Norm of Geom. B-factor gradient 136. Product of X_ray and Geom posit. gradients -0.123E+08 Cosine of angle between them -0.284 Product of X_ray and Geom B-fact gradients 0.231E+07 Cosine of angle between them 0.032 Residuals: XRAY= 0.1104E+07 GEOM= 7166. TOTAL= 0.1111E+07 function value 1110801.1 ------------------------------------------------------------------------------- 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 4.992 8.334 Long range B values: others 1276 4.739 7.993 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.927, B = -1.351 Babinet"s bulk solvent: scale = 0.189, B = 153.554 Partial structure 1: scale = 0.426, B = 33.291 Overall anisotropic scale factors B11 = 0.14 B22 = 0.14 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 11. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 11. v. resln :N:1,6,7,11,12: :Cycle 11. and v. resln :N:1,4,5,9,10: :Cycle 11. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 613.7 593.0 0.22 0.30 14 394.2 424.4 0.20 0.26 0.040 535 100.00 513.2 541.8 0.20 0.27 34 542.4 593.6 0.21 0.33 0.067 672 100.00 571.9 543.7 0.18 0.23 32 523.6 527.6 0.18 0.24 0.094 779 99.75 467.5 435.6 0.19 0.23 31 497.0 446.1 0.21 0.23 0.121 879 100.00 340.8 333.9 0.19 0.23 43 322.0 313.7 0.18 0.24 0.148 958 100.00 280.4 288.2 0.19 0.22 42 260.9 257.9 0.21 0.24 0.174 1040 100.00 260.6 261.9 0.17 0.19 38 277.6 292.2 0.14 0.17 0.201 1096 100.00 241.2 232.8 0.16 0.18 65 231.9 228.7 0.19 0.21 0.228 1185 100.00 218.0 212.9 0.16 0.17 56 229.5 218.8 0.15 0.16 0.255 1205 100.00 188.0 181.4 0.16 0.17 82 184.2 182.0 0.20 0.21 0.281 1298 100.00 161.2 157.1 0.17 0.17 59 155.4 154.5 0.20 0.20 0.308 1337 100.00 139.5 138.6 0.18 0.17 76 135.8 131.3 0.20 0.21 0.335 1403 100.00 125.3 122.2 0.17 0.17 88 119.3 119.0 0.22 0.22 0.362 1434 100.00 117.7 112.5 0.17 0.16 74 114.5 107.0 0.19 0.18 0.388 1507 100.00 109.7 105.9 0.17 0.16 76 105.0 105.9 0.22 0.20 0.415 1532 100.00 98.6 95.0 0.16 0.15 97 98.8 90.9 0.20 0.19 0.442 1579 100.00 92.8 89.1 0.17 0.15 92 94.1 88.6 0.20 0.19 0.469 1633 100.00 86.8 83.1 0.17 0.15 109 86.8 84.5 0.22 0.20 0.495 1576 93.50 75.3 73.7 0.18 0.16 79 78.5 76.5 0.22 0.18 0.522 1250 72.50 72.2 71.1 0.17 0.15 63 69.1 63.1 0.22 0.20 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.910 140 0.837 319 0.878 0.963 0.0405 376 0.925 159 0.827 535 0.896 0.975 0.0672 518 0.938 154 0.831 672 0.913 0.984 0.0940 623 0.924 156 0.850 779 0.909 0.991 0.1208 716 0.869 163 0.778 879 0.852 0.992 0.1475 800 0.892 158 0.763 958 0.871 0.963 0.1743 883 0.921 157 0.801 1040 0.903 0.953 0.2010 934 0.926 162 0.863 1096 0.916 0.977 0.2278 1022 0.930 163 0.862 1185 0.921 0.987 0.2546 1048 0.910 157 0.823 1205 0.898 0.981 0.2813 1136 0.891 162 0.812 1298 0.881 0.969 0.3081 1176 0.893 161 0.788 1337 0.880 0.964 0.3349 1243 0.893 160 0.831 1403 0.886 0.970 0.3616 1269 0.898 165 0.760 1434 0.882 0.982 0.3884 1347 0.892 160 0.847 1507 0.887 0.984 0.4151 1380 0.898 152 0.794 1532 0.887 0.981 0.4419 1421 0.896 158 0.820 1579 0.888 0.987 0.4687 1477 0.890 156 0.834 1633 0.885 0.982 0.4954 1447 0.868 131 0.746 1578 0.857 0.966 0.5222 1161 0.879 87 0.823 1248 0.875 0.963 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.1765 Free R factor = 0.1955 Overall weighted R factor = 0.1874 Free weighted R factor = 0.2095 Overall weighted R2 factor = 0.2511 Free weighted R2 factor = 0.2790 Overall correlation coefficient = 0.9560 Free correlation coefficient = 0.9458 Cruickshanks DPI for coordinate error= 0.0606 DPI based on free R factor = 0.0603 Overall figure of merit = 0.8872 ML based su of positional parameters = 0.0354 ML based su of thermal parameters = 1.6604 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 5.00000007E-02 Gamma decreased to 3.99999991E-02 fvalues 112483.31 7166.0430 1105907.0 1131999.1 CGMAT cycle number = 2 fast hessian tabulation Weight matrix 3.8690114 Actual weight 10.000000 is applied to the X-ray term function value 1096807.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.021 0.019 Bond distances: others 962 0.001 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.925, B = -0.720 Babinet"s bulk solvent: scale = 0.180, B = 153.534 Partial structure 1: scale = 0.427, B = 32.143 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 = 0.1675 Free R factor = 0.1904 Overall figure of merit = 0.8936 ----------------------------------------------------------------------------- Trying gamma equal 3.99999991E-02 Gamma decreased to 3.09090894E-02 fvalues 109870.97 5734.7017 1089699.4 1104444.4 CGMAT cycle number = 3 fast hessian tabulation Weight matrix 4.3409519 Actual weight 10.000000 is applied to the X-ray term function value 1086855.4 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.005 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.923, B = -0.021 Babinet"s bulk solvent: scale = 0.173, B = 153.519 Partial structure 1: scale = 0.427, B = 31.120 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 = 0.1612 Free R factor = 0.1868 Overall figure of merit = 0.8994 ----------------------------------------------------------------------------- Trying gamma equal 3.09090894E-02 Gamma decreased to 2.26446260E-02 fvalues 108117.51 5685.4990 1084878.0 1086860.6 CGMAT cycle number = 4 fast hessian tabulation Weight matrix 4.0741229 Actual weight 9.0909090 is applied to the X-ray term function value 986273.88 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.023 0.019 Bond distances: others 962 0.006 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.921, B = -0.027 Babinet"s bulk solvent: scale = 0.171, B = 153.514 Partial structure 1: scale = 0.427, B = 30.796 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 = 0.1595 Free R factor = 0.1855 Overall figure of merit = 0.9011 ----------------------------------------------------------------------------- Trying gamma equal 2.26446260E-02 Gamma decreased to 1.51314782E-02 fvalues 107863.41 5713.8003 985832.88 986290.19 CGMAT cycle number = 5 fast hessian tabulation Weight matrix 3.7343411 Actual weight 8.2644625 is applied to the X-ray term function value 896603.69 ------------------------------------------------------------------------------- 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 = 0.921, B = -0.023 Babinet"s bulk solvent: scale = 0.170, B = 153.514 Partial structure 1: scale = 0.428, B = 30.799 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 = 0.1592 Free R factor = 0.1851 Overall figure of merit = 0.9016 ----------------------------------------------------------------------------- Trying gamma equal 1.51314782E-02 Gamma decreased to 8.30134377E-03 fvalues 107810.36 5622.4238 896335.19 896617.06 CGMAT cycle number = 6 fast hessian tabulation Weight matrix 3.7626138 Actual weight 8.2644625 is applied to the X-ray term function value 896256.81 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.920, B = -0.021 Babinet"s bulk solvent: scale = 0.168, B = 153.514 Partial structure 1: scale = 0.428, B = 30.806 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 = 0.1591 Free R factor = 0.1847 Overall figure of merit = 0.9020 ----------------------------------------------------------------------------- Trying gamma equal 8.30134377E-03 Gamma decreased to 2.09213095E-03 fvalues 107783.25 5501.7769 896065.56 896272.38 CGMAT cycle number = 7 fast hessian tabulation Weight matrix 3.7739828 Actual weight 8.2644625 is applied to the X-ray term function value 896069.06 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.920, B = -0.019 Babinet"s bulk solvent: scale = 0.168, B = 153.515 Partial structure 1: scale = 0.428, B = 30.856 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 = 0.1589 Free R factor = 0.1848 Overall figure of merit = 0.9022 ----------------------------------------------------------------------------- Trying gamma equal 2.09213095E-03 Gamma decreased to 0.0000000 fvalues 107768.05 5434.8384 895961.13 896079.81 CGMAT cycle number = 8 fast hessian tabulation Weight matrix 3.7790251 Actual weight 8.2644625 is applied to the X-ray term function value 895972.56 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.920, B = -0.016 Babinet"s bulk solvent: scale = 0.166, B = 153.512 Partial structure 1: scale = 0.428, B = 30.633 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 = 0.1588 Free R factor = 0.1849 Overall figure of merit = 0.9023 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 2.56579034E-02 Gamma decreased to 2.05263235E-02 fvalues 107760.64 5396.1538 895861.56 895979.94 CGMAT cycle number = 9 fast hessian tabulation Weight matrix 3.7851777 Actual weight 8.2644625 is applied to the X-ray term function value 895881.06 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.013 Babinet"s bulk solvent: scale = 0.166, B = 153.512 Partial structure 1: scale = 0.429, B = 30.631 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 = 0.1588 Free R factor = 0.1849 Overall figure of merit = 0.9024 ----------------------------------------------------------------------------- Trying gamma equal 2.05263235E-02 Gamma decreased to 1.58612505E-02 fvalues 107754.01 5361.7007 895809.13 895890.63 CGMAT cycle number = 10 fast hessian tabulation Weight matrix 3.7950871 Actual weight 8.2644625 is applied to the X-ray term function value 895778.31 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.009 Babinet"s bulk solvent: scale = 0.166, B = 153.509 Partial structure 1: scale = 0.428, B = 30.431 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 = 0.1587 Free R factor = 0.1848 Overall figure of merit = 0.9026 ----------------------------------------------------------------------------- Trying gamma equal 1.58612505E-02 Gamma decreased to 1.16202747E-02 fvalues 107743.30 5341.6475 895728.06 895782.06 CGMAT cycle number = 11 fast hessian tabulation Weight matrix 3.7967482 Actual weight 8.2644625 is applied to the X-ray term function value 895754.69 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.007 Babinet"s bulk solvent: scale = 0.165, B = 153.510 Partial structure 1: scale = 0.428, B = 30.462 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 = 0.1587 Free R factor = 0.1848 Overall figure of merit = 0.9026 ----------------------------------------------------------------------------- Trying gamma equal 1.16202747E-02 Gamma decreased to 7.76484236E-03 fvalues 107741.63 5331.6147 895730.00 895758.25 CGMAT cycle number = 12 fast hessian tabulation Weight matrix 3.8064208 Actual weight 8.2644625 is applied to the X-ray term function value 895718.50 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.004 Babinet"s bulk solvent: scale = 0.165, B = 153.509 Partial structure 1: scale = 0.428, B = 30.440 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 = 0.1587 Free R factor = 0.1848 Overall figure of merit = 0.9027 ----------------------------------------------------------------------------- Trying gamma equal 7.76484236E-03 Gamma decreased to 4.25990392E-03 fvalues 107737.39 5328.1738 895690.88 895719.81 CGMAT cycle number = 13 fast hessian tabulation Weight matrix 3.4584599 Actual weight 7.5131474 is applied to the X-ray term function value 814790.94 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.007 Babinet"s bulk solvent: scale = 0.165, B = 153.509 Partial structure 1: scale = 0.428, B = 30.437 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 = 0.1587 Free R factor = 0.1848 Overall figure of merit = 0.9027 ----------------------------------------------------------------------------- Trying gamma equal 4.25990392E-03 Gamma decreased to 1.07359642E-03 fvalues 107740.73 5322.1357 814814.06 814794.13 fvalues 107740.73 5322.1357 814792.31 814794.13 CGMAT cycle number = 14 fast hessian tabulation Weight matrix 3.1466434 Actual weight 6.8301339 is applied to the X-ray term function value 741202.50 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.022 0.019 Bond distances: others 962 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.919, B = -0.008 Babinet"s bulk solvent: scale = 0.164, B = 153.509 Partial structure 1: scale = 0.428, B = 30.417 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 = 0.1587 Free R factor = 0.1848 Overall figure of merit = 0.9027 ----------------------------------------------------------------------------- Trying gamma equal 1.07359642E-03 Gamma decreased to 0.0000000 fvalues 107746.27 5287.5947 741191.63 741209.06 CGMAT cycle number = 15 fast hessian tabulation Weight matrix 3.1434772 Actual weight 6.8301339 is applied to the X-ray term function value 741246.50 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.021 0.019 Bond distances: others 962 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.918, B = -0.010 Babinet"s bulk solvent: scale = 0.164, B = 153.509 Partial structure 1: scale = 0.428, B = 30.420 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 = 0.1589 Free R factor = 0.1848 Overall figure of merit = 0.9027 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 1.31665589E-02 Gamma decreased to 1.05332471E-02 fvalues 107771.84 5154.5078 741226.50 741250.63 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\r42.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= 0.7362E+06 GEOM= 5063. TOTAL= 0.7413E+06 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1037 0.021 0.019 Bond distances: others 962 0.003 0.020 Bond angles : refined atoms 1408 2.098 1.903 Bond angles : others 2180 0.995 3.007 Torsion angles, period 1. refined 132 6.359 5.000 Torsion angles, period 2. refined 51 36.414 22.745 Torsion angles, period 3. refined 169 12.215 15.000 Torsion angles, period 3. others 8 4.152 15.000 Torsion angles, period 4. refined 12 23.914 15.000 Chiral centres: refined atoms 146 0.141 0.200 Planar groups: refined atoms 1225 0.011 0.020 Planar groups: others 277 0.001 0.020 VDW repulsions: refined_atoms 312 0.266 0.200 VDW repulsions.others 890 0.176 0.200 VDW; torsion: refined_atoms 522 0.187 0.200 VDW; torsion.others 581 0.087 0.200 HBOND: refined_atoms 17 0.143 0.200 Metal-ion: refined_atoms 4 0.138 0.200 VDW repulsions: symmetry: refined_atoms 18 0.258 0.200 VDW repulsions: symmetry: others 26 0.143 0.200 HBOND: symmetry: refined_atoms 2 0.098 0.200 M. chain bond B values: refined atoms 519 1.087 0.745 M. chain bond B values: others 518 1.051 0.742 M. chain angle B values: refined atoms 648 1.584 1.120 M. chain angle B values: others 649 1.586 1.123 S. chain bond B values: refined atoms 518 2.157 0.954 S. chain bond B values: others 518 2.156 0.953 S. chain angle B values: refined atoms 758 2.937 1.358 S. chain angle B values: others 758 2.933 1.357 Long range B values: refined atoms 1306 4.040 6.869 Long range B values: others 1267 3.926 6.556 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.918, B = -0.008 Babinet"s bulk solvent: scale = 0.163, B = 153.509 Partial structure 1: scale = 0.429, B = 30.446 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 26. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 26. v. resln :N:1,6,7,11,12: :Cycle 26. and v. resln :N:1,4,5,9,10: :Cycle 26. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 619.9 599.5 0.21 0.30 14 398.2 435.1 0.20 0.25 0.040 535 100.00 518.4 545.8 0.19 0.26 34 547.8 590.4 0.20 0.32 0.067 672 100.00 577.6 550.8 0.17 0.22 32 528.9 530.0 0.19 0.23 0.094 779 99.75 472.2 441.8 0.18 0.22 31 502.0 441.3 0.21 0.23 0.121 879 100.00 344.3 338.3 0.18 0.22 43 325.2 314.1 0.18 0.23 0.148 958 100.00 283.2 290.8 0.18 0.20 42 263.5 257.8 0.20 0.23 0.174 1040 100.00 263.2 266.2 0.16 0.18 38 280.4 296.5 0.15 0.19 0.201 1096 100.00 243.7 237.2 0.15 0.17 65 234.3 233.4 0.18 0.19 0.228 1185 100.00 220.2 216.3 0.14 0.16 56 231.9 218.4 0.15 0.16 0.255 1205 100.00 189.9 185.3 0.15 0.15 82 186.1 185.1 0.20 0.21 0.281 1298 100.00 162.8 160.1 0.15 0.15 59 156.9 156.5 0.19 0.20 0.308 1337 100.00 140.9 141.0 0.15 0.15 76 137.2 136.3 0.18 0.18 0.335 1403 100.00 126.5 124.3 0.15 0.14 88 120.5 119.1 0.21 0.20 0.362 1434 100.00 118.9 114.8 0.14 0.13 74 115.6 108.3 0.17 0.17 0.388 1507 100.00 110.8 107.4 0.14 0.13 76 106.1 104.3 0.18 0.16 0.415 1532 100.00 99.6 95.7 0.13 0.12 97 99.8 92.3 0.17 0.16 0.442 1579 100.00 93.8 90.0 0.13 0.12 92 95.0 89.1 0.16 0.16 0.469 1633 100.00 87.7 84.3 0.13 0.12 109 87.7 83.5 0.18 0.16 0.495 1576 93.50 76.0 74.7 0.15 0.13 79 79.3 76.1 0.20 0.17 0.522 1250 72.50 72.9 71.8 0.14 0.12 63 69.8 63.7 0.21 0.18 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 26. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 26. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.909 140 0.829 319 0.874 0.968 0.0405 376 0.926 159 0.824 535 0.895 0.979 0.0672 518 0.939 154 0.836 672 0.915 0.986 0.0940 623 0.926 156 0.856 779 0.912 0.992 0.1208 716 0.876 163 0.783 879 0.859 0.992 0.1475 800 0.899 158 0.766 958 0.877 0.963 0.1743 883 0.926 157 0.801 1040 0.907 0.951 0.2010 934 0.927 162 0.844 1096 0.914 0.973 0.2278 1022 0.934 163 0.868 1185 0.925 0.985 0.2546 1048 0.912 157 0.853 1205 0.905 0.981 0.2813 1136 0.890 162 0.817 1298 0.881 0.969 0.3081 1176 0.909 161 0.818 1337 0.898 0.964 0.3349 1243 0.911 160 0.844 1403 0.903 0.970 0.3616 1269 0.904 165 0.775 1434 0.889 0.984 0.3884 1347 0.917 160 0.881 1507 0.913 0.991 0.4151 1380 0.924 152 0.828 1532 0.914 0.993 0.4419 1421 0.930 158 0.854 1579 0.923 1.005 0.4687 1477 0.919 156 0.874 1633 0.915 0.992 0.4954 1447 0.902 131 0.791 1578 0.893 0.977 0.5222 1161 0.905 87 0.854 1248 0.902 0.971 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.1590 Free R factor = 0.1848 Overall weighted R factor = 0.1683 Free weighted R factor = 0.1966 Overall weighted R2 factor = 0.2339 Free weighted R2 factor = 0.2657 Overall correlation coefficient = 0.9615 Free correlation coefficient = 0.9493 Cruickshanks DPI for coordinate error= 0.0546 DPI based on free R factor = 0.0570 Overall figure of merit = 0.9027 ML based su of positional parameters = 0.0307 ML based su of thermal parameters = 1.4015 ----------------------------------------------------------------------------- Time in seconds: CPU = 0.00 Elapsed = 114.00 **** 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: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.1807 0.2006 0.881 111196. 6077.7 0.0 0.0 0.0 0.0 0.0 1 0.1787 0.1980 0.884 110791. 6056.0 0.0 0.0 0.0 0.0 0.0 2 0.1778 0.1969 0.886 110612. 6046.1 0.0 0.0 0.0 0.0 0.0 3 0.1774 0.1964 0.886 110529. 6041.3 0.0 0.0 0.0 0.0 0.0 4 0.1771 0.1961 0.886 110482. 6038.3 0.0 0.0 0.0 0.0 0.0 5 0.1770 0.1959 0.887 110449. 6036.0 0.0 0.0 0.0 0.0 0.0 6 0.1769 0.1957 0.887 110429. 6034.5 0.0 0.0 0.0 0.0 0.0 7 0.1768 0.1956 0.887 110416. 6033.4 0.0 0.0 0.0 0.0 0.0 8 0.1768 0.1954 0.887 110405. 6032.4 0.0 0.0 0.0 0.0 0.0 9 0.1767 0.1954 0.887 110399. 6031.9 0.0 0.0 0.0 0.0 0.0 10 0.1765 0.1955 0.887 110364. 6031.4 0.0219 1.149 2.146 1.094 0.133 11 0.1675 0.1904 0.894 109107. 5982.5 0.0212 1.095 2.107 1.075 0.134 12 0.1612 0.1868 0.899 108117. 5941.2 0.0224 1.149 2.157 1.105 0.140 13 0.1595 0.1855 0.901 107862. 5930.0 0.0230 1.181 2.204 1.133 0.144 14 0.1592 0.1851 0.902 107809. 5926.9 0.0228 1.169 2.199 1.130 0.144 15 0.1591 0.1847 0.902 107781. 5924.5 0.0223 1.144 2.180 1.120 0.144 16 0.1589 0.1848 0.902 107767. 5923.9 0.0221 1.131 2.169 1.114 0.144 17 0.1588 0.1849 0.902 107760. 5923.6 0.0220 1.124 2.163 1.111 0.144 18 0.1588 0.1849 0.902 107753. 5923.5 0.0219 1.121 2.160 1.110 0.144 19 0.1587 0.1848 0.903 107743. 5922.6 0.0219 1.119 2.159 1.109 0.144 20 0.1587 0.1848 0.903 107741. 5922.8 0.0219 1.119 2.158 1.109 0.145 21 0.1587 0.1848 0.903 107737. 5922.6 0.0219 1.120 2.159 1.109 0.145 22 0.1587 0.1848 0.903 107740. 5923.4 0.0219 1.120 2.160 1.110 0.145 23 0.1587 0.1848 0.903 107745. 5923.1 0.0217 1.111 2.151 1.105 0.145 24 0.1589 0.1848 0.903 107771. 5924.0 0.0210 1.077 2.118 1.086 0.143 25 0.1590 0.1848 0.903 107785. 5924.4 0.0207 1.057 2.098 1.075 0.141 $$ $TEXT:Result: $$ Final results $$ Initial Final R factor 0.1807 0.1590 R free 0.2006 0.1848 Rms BondLength 0.0219 0.0207 Rms BondAngle 2.1456 2.0978 Rms ChirVolume 0.1332 0.1414 $$
Refmac_5.7.0032: End of Refmac_5.7.0032 Times: User: 0.0s System: 0.0s Elapsed: 2:07
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CCP4i: Writing final coordinates (XYZOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r42.pdb
CCP4i: Writing final phases (HKLOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r42.mtz
CCP4i: Writing final TLS (TLSOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r42.tls
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