Summary:
Initial | After 20 cycles | |
---|---|---|
R factor | 0.5061 | 0.3819 |
Rfree | 0.5138 | 0.3942 |
RMSD Bond Length | 0.0 | 0.0212 |
RMSD Bond Angle | 0.0 | 2.478 |
RMSD Chiral Centre | 0.0 | 0.462 |
Result:
Initial | Final | |
---|---|---|
R factor | 0.5061 | 0.3819 |
R free | 0.5138 | 0.3942 |
Rms BondLength | 0.0301 | 0.0212 |
Rms BondAngle | 2.1372 | 2.4784 |
Rms ChirVolume | 0.6904 | 0.4615 |
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 21. Rfactor analysis, F distribution v resln Cycle 21. 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 21. Rfactor analysis, F distribution v resln Cycle 21. 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: 18:35:43 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 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\mr1.pdb Output coordinate file. Logical name - XYZOUT actual file name - C:/SOLVE_REFINE/lizozim/mr-refine-build\r11.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\r11.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\mr1.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 : 917 Number of residues : 129 Number of chains : 1 I am reading library. Please wait. mon_lib.cif WARNING : large distance for conn:TRANS dist = 5.748 ch:AA res: 47 THR --> 48 ASP ideal_dist= 1.329 WARNING : reverse conn, will not be used WARNING : link:SS is found dist = 2.026 ideal_dist= 2.031 ch:AA res: 6 CYS at:SG .->AA res: 127 CYS at:SG . WARNING : link:SS is found dist = 2.035 ideal_dist= 2.031 ch:AA res: 30 CYS at:SG .->AA res: 115 CYS at:SG . WARNING : link:SS is found dist = 2.021 ideal_dist= 2.031 ch:AA res: 64 CYS at:SG .->AA res: 80 CYS at:SG . WARNING : link:SS is found dist = 2.033 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 MET 12 AA is missing in the structure ATTENTION: atom:CE1 HIS 15 AA is missing in the structure ATTENTION: atom:NE2 HIS 15 AA is missing in the structure ATTENTION: atom:CD2 LEU 17 AA is missing in the structure ATTENTION: atom:CB ASN 19 AA is missing in the structure ATTENTION: atom:CG ASN 19 AA is missing in the structure ATTENTION: atom:OD1 ASN 19 AA is missing in the structure ATTENTION: atom:ND2 ASN 19 AA is missing in the structure ATTENTION: atom:CE1 TYR 23 AA is missing in the structure ATTENTION: atom:CZ TYR 23 AA is missing in the structure ATTENTION: atom:OH TYR 23 AA is missing in the structure ATTENTION: atom:CE2 TYR 23 AA is missing in the structure ATTENTION: atom:CD2 TYR 23 AA is missing in the structure ATTENTION: atom:CG2 VAL 29 AA is missing in the structure ATTENTION: atom:CE1 PHE 34 AA is missing in the structure ATTENTION: atom:CZ PHE 34 AA is missing in the structure ATTENTION: atom:CE2 PHE 34 AA is missing in the structure ATTENTION: atom:CB ASN 37 AA is missing in the structure ATTENTION: atom:CG ASN 37 AA is missing in the structure ATTENTION: atom:OD1 ASN 37 AA is missing in the structure ... and more ... Number of chains : 1 Total number of monomers : 129 Number of atoms : 1969 Number of missing atoms : 76 Number of rebuilt atoms : 844 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: 1746 0 1746 Angles: 3104 0 3104 Chirals: 132 0 132 Planes: 302 0 302 Torsions: 706 0 706 --------------------------------------- **** 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 0.60431194 20.233475 8.7738771 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 = 0.847, B = -10.389 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.414, B = 13.807 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 376.9 341.6 0.37 0.52 14 246.5 266.1 0.57 0.72 0.040 535 100.00 394.8 394.8 0.41 0.56 34 419.1 402.0 0.43 0.63 0.067 672 100.00 482.5 376.9 0.47 0.56 32 412.0 365.2 0.44 0.59 0.094 779 99.75 409.3 316.9 0.48 0.54 31 421.2 303.3 0.55 0.59 0.121 879 100.00 303.9 264.2 0.52 0.57 43 311.5 265.0 0.55 0.63 0.148 958 100.00 256.3 221.5 0.53 0.55 42 231.2 197.3 0.62 0.63 0.174 1040 100.00 242.2 202.4 0.52 0.53 38 255.9 219.9 0.43 0.48 0.201 1096 100.00 225.0 190.2 0.52 0.52 65 214.8 194.4 0.54 0.54 0.228 1185 100.00 205.8 170.6 0.50 0.50 56 224.3 186.7 0.39 0.39 0.255 1205 100.00 179.0 145.4 0.53 0.51 82 186.9 149.8 0.48 0.46 0.281 1298 100.00 154.4 126.3 0.53 0.50 59 152.8 129.5 0.64 0.60 0.308 1337 100.00 134.3 110.8 0.53 0.49 76 137.0 103.0 0.54 0.50 0.335 1403 100.00 121.5 99.7 0.52 0.49 88 114.2 83.0 0.59 0.56 0.362 1434 100.00 114.0 88.7 0.53 0.50 74 118.5 88.1 0.51 0.48 0.388 1507 100.00 107.3 82.1 0.53 0.49 76 102.8 82.6 0.48 0.46 0.415 1532 100.00 97.2 76.0 0.52 0.49 97 94.8 70.2 0.57 0.53 0.442 1579 100.00 91.4 67.1 0.53 0.50 92 92.9 68.1 0.46 0.45 0.469 1633 100.00 85.9 61.8 0.55 0.53 109 80.2 60.6 0.56 0.53 0.495 1576 93.50 75.6 56.2 0.54 0.52 79 81.6 61.3 0.53 0.51 0.522 1250 72.50 73.4 52.6 0.54 0.52 63 73.2 52.0 0.55 0.54 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.634 140 0.537 319 0.591 0.840 0.0405 376 0.633 159 0.551 535 0.609 0.791 0.0672 518 0.632 154 0.505 672 0.603 0.756 0.0940 623 0.522 156 0.470 779 0.512 0.726 0.1208 716 0.385 163 0.332 879 0.375 0.693 0.1475 800 0.343 158 0.251 958 0.328 0.618 0.1743 883 0.393 157 0.305 1040 0.380 0.615 0.2010 934 0.502 162 0.400 1096 0.487 0.719 0.2278 1022 0.491 163 0.433 1185 0.483 0.726 0.2546 1048 0.425 157 0.362 1205 0.417 0.659 0.2813 1136 0.353 162 0.295 1298 0.346 0.583 0.3081 1176 0.293 161 0.229 1337 0.285 0.530 0.3349 1243 0.301 160 0.229 1403 0.292 0.487 0.3616 1269 0.335 165 0.255 1434 0.326 0.544 0.3884 1347 0.365 160 0.302 1507 0.358 0.578 0.4151 1380 0.414 152 0.336 1532 0.406 0.619 0.4419 1421 0.333 158 0.298 1579 0.329 0.545 0.4687 1477 0.320 156 0.255 1633 0.314 0.536 0.4954 1447 0.352 131 0.238 1578 0.342 0.629 0.5222 1161 0.219 87 0.193 1248 0.217 0.422 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.5061 Free R factor = 0.5138 Overall weighted R factor = 0.5190 Free weighted R factor = 0.5298 Overall weighted R2 factor = 0.6421 Free weighted R2 factor = 0.6624 Overall correlation coefficient = 0.6470 Free correlation coefficient = 0.6209 Cruickshanks DPI for coordinate error= 0.1411 DPI based on free R factor = 0.1432 Overall figure of merit = 0.3738 ML based su of positional parameters = 0.3159 ML based su of thermal parameters = 17.2991 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.003 0.002 0.008 -0.001 0.003 0.001 L tensor ( 1) = 0.373 0.178 0.333 -0.124 0.090 -0.001 S tensor ( 1) = 0.016 -0.016 0.011 -0.003 -0.002 -0.006 0.009 0.017 ***TLS refinement cycle*** 2 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.848, B = -11.612 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.416, B = 15.969 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.5046 Free R factor = 0.5123 Overall figure of merit = 0.3525 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.008 0.005 0.019 -0.001 0.009 0.001 L tensor ( 1) = 1.077 0.536 1.029 -0.406 0.249 -0.001 S tensor ( 1) = 0.054 -0.051 0.032 -0.010 -0.006 -0.018 0.029 0.054 ***TLS refinement cycle*** 3 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.853, B = -13.529 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.417, B = 18.505 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.5023 Free R factor = 0.5085 Overall figure of merit = 0.3501 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.014 0.008 0.021 -0.003 0.013 -0.001 L tensor ( 1) = 1.605 0.849 1.547 -0.634 0.388 -0.011 S tensor ( 1) = 0.086 -0.081 0.048 -0.017 -0.008 -0.027 0.042 0.083 ***TLS refinement cycle*** 4 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.860, B = -14.641 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.418, B = 19.263 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.5009 Free R factor = 0.5056 Overall figure of merit = 0.3541 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.019 0.011 0.025 -0.005 0.017 -0.003 L tensor ( 1) = 1.973 1.071 1.915 -0.813 0.496 -0.026 S tensor ( 1) = 0.113 -0.107 0.059 -0.022 -0.009 -0.034 0.050 0.105 ***TLS refinement cycle*** 5 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.866, B = -15.441 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.419, B = 19.243 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.5003 Free R factor = 0.5037 Overall figure of merit = 0.3565 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.024 0.013 0.031 -0.007 0.022 -0.005 L tensor ( 1) = 2.234 1.247 2.174 -0.943 0.586 -0.035 S tensor ( 1) = 0.134 -0.127 0.065 -0.027 -0.010 -0.039 0.055 0.119 ***TLS refinement cycle*** 6 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.871, B = -16.081 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.421, B = 20.578 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.5000 Free R factor = 0.5026 Overall figure of merit = 0.3575 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.029 0.016 0.035 -0.010 0.026 -0.006 L tensor ( 1) = 2.433 1.391 2.363 -1.040 0.657 -0.032 S tensor ( 1) = 0.152 -0.145 0.070 -0.031 -0.010 -0.043 0.057 0.130 ***TLS refinement cycle*** 7 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.876, B = -16.621 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.422, B = 21.933 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4999 Free R factor = 0.5017 Overall figure of merit = 0.3581 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.032 0.021 0.040 -0.012 0.029 -0.007 L tensor ( 1) = 2.578 1.506 2.506 -1.107 0.711 -0.018 S tensor ( 1) = 0.168 -0.159 0.072 -0.035 -0.011 -0.045 0.058 0.137 ***TLS refinement cycle*** 8 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.879, B = -17.110 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.422, B = 21.904 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4999 Free R factor = 0.5013 Overall figure of merit = 0.3586 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.036 0.026 0.044 -0.015 0.033 -0.008 L tensor ( 1) = 2.688 1.594 2.608 -1.153 0.749 0.004 S tensor ( 1) = 0.181 -0.170 0.074 -0.038 -0.011 -0.047 0.057 0.143 ***TLS refinement cycle*** 9 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.881, B = -17.553 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.422, B = 22.410 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4999 Free R factor = 0.5009 Overall figure of merit = 0.3589 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.039 0.031 0.049 -0.017 0.035 -0.008 L tensor ( 1) = 2.768 1.660 2.684 -1.181 0.776 0.032 S tensor ( 1) = 0.192 -0.180 0.076 -0.041 -0.011 -0.049 0.056 0.147 ***TLS refinement cycle*** 10 fast hessian tabulation ----------------------------------------------------------------------------- Overall : scale = 0.883, B = -17.944 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.423, B = 23.066 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 644.4 599.9 0.37 0.53 14 413.9 466.0 0.58 0.74 0.040 535 100.00 538.9 547.8 0.41 0.56 34 569.5 555.9 0.41 0.61 0.067 672 100.00 600.5 475.9 0.46 0.56 32 549.8 507.9 0.42 0.58 0.094 779 99.75 490.9 377.2 0.49 0.54 31 521.9 369.7 0.54 0.57 0.121 879 100.00 357.9 309.1 0.51 0.57 43 338.1 284.0 0.58 0.66 0.148 958 100.00 294.4 250.4 0.52 0.53 42 273.9 224.9 0.59 0.58 0.174 1040 100.00 273.6 226.3 0.51 0.53 38 291.5 254.8 0.46 0.51 0.201 1096 100.00 253.3 212.0 0.51 0.51 65 243.5 218.0 0.52 0.53 0.228 1185 100.00 228.9 187.4 0.50 0.50 56 241.0 202.9 0.43 0.44 0.255 1205 100.00 197.4 157.4 0.52 0.50 82 193.5 159.6 0.48 0.47 0.281 1298 100.00 169.2 135.8 0.53 0.50 59 163.1 131.6 0.61 0.57 0.308 1337 100.00 146.5 122.8 0.52 0.49 76 142.6 106.7 0.50 0.47 0.335 1403 100.00 131.5 108.8 0.52 0.49 88 125.2 97.7 0.55 0.50 0.362 1434 100.00 123.6 98.4 0.52 0.48 74 120.2 91.3 0.50 0.48 0.388 1507 100.00 115.2 89.8 0.51 0.48 76 110.2 92.7 0.47 0.45 0.415 1532 100.00 103.6 83.7 0.51 0.47 97 103.8 78.1 0.54 0.50 0.442 1579 100.00 97.5 75.5 0.52 0.49 92 98.8 77.7 0.43 0.42 0.469 1633 100.00 91.1 69.9 0.54 0.51 109 91.2 73.4 0.49 0.47 0.495 1576 93.50 79.0 64.3 0.53 0.50 79 82.4 67.5 0.51 0.48 0.522 1250 72.50 75.8 61.3 0.52 0.49 63 72.6 55.9 0.51 0.50 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.643 140 0.547 319 0.601 0.828 0.0405 376 0.629 159 0.553 535 0.606 0.765 0.0672 518 0.622 154 0.496 672 0.593 0.719 0.0940 623 0.498 156 0.442 779 0.487 0.681 0.1208 716 0.361 163 0.310 879 0.352 0.646 0.1475 800 0.331 158 0.248 958 0.317 0.599 0.1743 883 0.397 157 0.312 1040 0.384 0.614 0.2010 934 0.505 162 0.394 1096 0.489 0.716 0.2278 1022 0.489 163 0.425 1185 0.480 0.725 0.2546 1048 0.428 157 0.352 1205 0.418 0.659 0.2813 1136 0.306 162 0.249 1298 0.299 0.488 0.3081 1176 0.199 161 0.153 1337 0.194 0.345 0.3349 1243 0.303 160 0.233 1403 0.295 0.474 0.3616 1269 0.350 165 0.271 1434 0.341 0.544 0.3884 1347 0.375 160 0.328 1507 0.370 0.586 0.4151 1380 0.445 152 0.356 1532 0.436 0.644 0.4419 1421 0.364 158 0.332 1579 0.360 0.547 0.4687 1477 0.370 156 0.283 1633 0.361 0.555 0.4954 1447 0.252 131 0.167 1578 0.245 0.383 0.5222 1161 0.084 87 0.060 1248 0.083 0.145 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.4998 Free R factor = 0.5006 Overall weighted R factor = 0.5112 Free weighted R factor = 0.5163 Overall weighted R2 factor = 0.6334 Free weighted R2 factor = 0.6502 Overall correlation coefficient = 0.6536 Free correlation coefficient = 0.6344 Cruickshanks DPI for coordinate error= 0.1393 DPI based on free R factor = 0.1395 Overall figure of merit = 0.3592 ML based su of positional parameters = 0.3675 ML based su of thermal parameters = 20.5754 ----------------------------------------------------------------------------- TLS group 1: chain A T tensor ( 1) = 0.041 0.036 0.053 -0.018 0.038 -0.008 L tensor ( 1) = 2.829 1.712 2.738 -1.195 0.797 0.063 S tensor ( 1) = 0.200 -0.187 0.077 -0.044 -0.011 -0.051 0.055 0.151 CGMAT cycle number = 1 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 12 MET CG . - A 12 MET SD . mod.= 1.577 id.= 1.803 dev= 0.226 sig.= 0.020 A 15 HIS CG . - A 15 HIS ND1 . mod.= 1.526 id.= 1.378 dev= -0.148 sig.= 0.011 A 15 HIS CG . - A 15 HIS CD2 . mod.= 1.534 id.= 1.354 dev= -0.180 sig.= 0.011 A 17 LEU CG . - A 17 LEU CD1 . mod.= 1.785 id.= 1.521 dev= -0.264 sig.= 0.020 A 23 TYR CG . - A 23 TYR CD1 . mod.= 1.609 id.= 1.389 dev= -0.220 sig.= 0.021 A 68 ARG NE . - A 68 ARG CZ . mod.= 1.497 id.= 1.329 dev= -0.168 sig.= 0.014 A 103 ASN CG . - A 103 ASN OD1 . mod.= 1.510 id.= 1.231 dev= -0.279 sig.= 0.019 A 105 MET CG . - A 105 MET SD . mod.= 1.488 id.= 1.803 dev= 0.315 sig.= 0.020 A 106 ASN CG . - A 106 ASN OD1 . mod.= 1.570 id.= 1.231 dev= -0.339 sig.= 0.019 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 15 HIS CB - A 15 HIS CD2 mod.= 109.89 id.= 131.20 dev= 21.313 sig.= 1.300 A 56 LEU HG - A 56 LEU CD1 mod.= 55.06 id.= 108.00 dev= 52.941 sig.= 3.000 A 77 ASN OD1 - A 77 ASN ND2 mod.= 106.25 id.= 122.60 dev= 16.349 sig.= 1.000 **** Chiral volume outliers **** Chiral volume deviations from the ideal >10.000Sigma will be monitored A 56 LEU CG mod.= -0.06 id.= -2.59 dev= -2.534 sig.= 0.200 A 98 ILE CB mod.= -2.57 id.= 2.64 dev= 5.211 sig.= 0.200 A 124 ILE CB mod.= -2.63 id.= 2.64 dev= 5.273 sig.= 0.200 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 15 HIS CG deviation= -0.35 sigma.= 0.02 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 10 ALA HB2 . - A 14 ARG HE . mod.= 0.683 id.= 2.400 dev= -1.72 sig.= 0.20 sym.= 6 0 0 1 type = 7 A 14 ARG NH1 . - A 14 ARG HH12. mod.= 0.739 id.= 2.750 dev= -2.01 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 2.99894605E-02 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 31.4 Norm of Geom. positional gradient 90.4 Norm of X_ray B-factor gradient 39.6 Norm of Geom. B-factor gradient 0.204E+04 Product of X_ray and Geom posit. gradients -0.217E+06 Cosine of angle between them -0.015 Product of X_ray and Geom B-fact gradients -0.443E+07 Cosine of angle between them -0.032 Residuals: XRAY= 0.1310E+07 GEOM= 0.1134E+05 TOTAL= 0.1322E+07 function value 1321536.5 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.030 0.019 Bond distances: others 814 0.000 0.020 Bond angles : refined atoms 1255 2.137 1.916 Bond angles : others 1849 4.248 3.009 Torsion angles, period 1. refined 127 6.193 5.000 Torsion angles, period 2. refined 38 37.334 23.421 Torsion angles, period 3. refined 138 12.665 15.000 Torsion angles, period 3. others 8 46.930 15.000 Torsion angles, period 4. refined 7 20.123 15.000 Chiral centres: refined atoms 132 0.690 0.200 Planar groups: refined atoms 1106 0.014 0.020 Planar groups: others 217 0.011 0.020 VDW repulsions: refined_atoms 172 0.213 0.200 VDW repulsions.others 643 0.225 0.200 VDW; torsion: refined_atoms 455 0.169 0.200 VDW; torsion.others 444 0.116 0.200 HBOND: refined_atoms 12 0.165 0.200 HBOND.others 1 0.114 0.200 VDW repulsions: symmetry: refined_atoms 22 0.605 0.200 VDW repulsions: symmetry: others 60 0.770 0.200 HBOND: symmetry: refined_atoms 1 0.101 0.200 M. chain bond B values: refined atoms 513 0.000 2.000 M. chain bond B values: others 512 0.000 2.000 M. chain angle B values: refined atoms 638 0.000 3.000 M. chain angle B values: others 639 0.000 3.000 S. chain bond B values: refined atoms 418 0.000 2.000 S. chain bond B values: others 417 0.000 2.000 S. chain angle B values: refined atoms 615 0.000 3.000 S. chain angle B values: others 615 0.000 3.000 Long range B values: refined atoms 1011 0.000 15.823 Long range B values: others 1012 0.000 15.827 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.885, B = -18.284 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.422, B = 23.106 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 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: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 643.3 599.6 0.37 0.53 14 413.2 466.0 0.58 0.74 0.040 535 100.00 538.0 547.0 0.41 0.56 34 568.5 554.9 0.41 0.61 0.067 672 100.00 599.5 475.2 0.46 0.56 32 548.9 507.6 0.42 0.58 0.094 779 99.75 490.1 376.5 0.49 0.54 31 521.0 369.1 0.54 0.57 0.121 879 100.00 357.3 308.5 0.51 0.57 43 337.5 283.4 0.58 0.66 0.148 958 100.00 293.9 249.9 0.52 0.53 42 273.5 224.3 0.59 0.58 0.174 1040 100.00 273.2 225.7 0.51 0.53 38 291.0 254.3 0.46 0.51 0.201 1096 100.00 252.9 211.5 0.51 0.51 65 243.1 217.3 0.52 0.53 0.228 1185 100.00 228.5 186.9 0.50 0.50 56 240.6 202.4 0.43 0.44 0.255 1205 100.00 197.1 157.0 0.52 0.50 82 193.1 159.0 0.48 0.47 0.281 1298 100.00 168.9 135.5 0.53 0.50 59 162.9 131.4 0.60 0.57 0.308 1337 100.00 146.2 122.5 0.52 0.49 76 142.4 106.5 0.50 0.47 0.335 1403 100.00 131.3 108.6 0.52 0.49 88 125.0 98.0 0.55 0.50 0.362 1434 100.00 123.4 98.2 0.52 0.48 74 120.0 91.3 0.50 0.47 0.388 1507 100.00 115.0 89.6 0.51 0.48 76 110.1 92.8 0.47 0.45 0.415 1532 100.00 103.4 83.6 0.51 0.47 97 103.6 77.9 0.54 0.50 0.442 1579 100.00 97.3 75.6 0.52 0.49 92 98.6 77.8 0.44 0.42 0.469 1633 100.00 91.0 69.9 0.54 0.51 109 91.0 73.5 0.49 0.47 0.495 1576 93.50 78.9 64.3 0.53 0.50 79 82.3 67.4 0.51 0.49 0.522 1250 72.50 75.7 61.5 0.52 0.49 63 72.4 56.3 0.51 0.49 $$ **** 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: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.644 140 0.547 319 0.601 0.828 0.0405 376 0.629 159 0.553 535 0.607 0.765 0.0672 518 0.622 154 0.496 672 0.594 0.719 0.0940 623 0.498 156 0.442 779 0.487 0.681 0.1208 716 0.361 163 0.310 879 0.352 0.646 0.1475 800 0.331 158 0.248 958 0.317 0.599 0.1743 883 0.397 157 0.312 1040 0.384 0.614 0.2010 934 0.505 162 0.394 1096 0.489 0.716 0.2278 1022 0.489 163 0.424 1185 0.480 0.725 0.2546 1048 0.428 157 0.351 1205 0.418 0.659 0.2813 1136 0.305 162 0.248 1298 0.298 0.488 0.3081 1176 0.199 161 0.153 1337 0.194 0.345 0.3349 1243 0.303 160 0.233 1403 0.295 0.474 0.3616 1269 0.351 165 0.271 1434 0.341 0.544 0.3884 1347 0.376 160 0.328 1507 0.371 0.586 0.4151 1380 0.445 152 0.356 1532 0.436 0.644 0.4419 1421 0.364 158 0.332 1579 0.361 0.547 0.4687 1477 0.370 156 0.283 1633 0.362 0.555 0.4954 1447 0.253 131 0.167 1578 0.246 0.383 0.5222 1161 0.085 87 0.060 1248 0.083 0.145 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.4998 Free R factor = 0.5005 Overall weighted R factor = 0.5112 Free weighted R factor = 0.5162 Overall weighted R2 factor = 0.6333 Free weighted R2 factor = 0.6501 Overall correlation coefficient = 0.6536 Free correlation coefficient = 0.6345 Cruickshanks DPI for coordinate error= 0.1518 DPI based on free R factor = 0.1395 Overall figure of merit = 0.3594 ML based su of positional parameters = 0.3688 ML based su of thermal parameters = 20.6568 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 5.00000007E-02 Gamma decreased to 3.99999991E-02 fvalues 131913.70 11340.911 1319599.3 1330478.0 CGMAT cycle number = 2 fast hessian tabulation Weight matrix 5.25540747E-02 Actual weight 10.000000 is applied to the X-ray term function value 1308296.5 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.018 0.019 Bond distances: others 814 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.899, B = -9.211 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.424, B = 15.671 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4784 Free R factor = 0.4807 Overall figure of merit = 0.4104 ----------------------------------------------------------------------------- Trying gamma equal 3.99999991E-02 Gamma decreased to 3.09090894E-02 fvalues 131241.28 6250.9507 1309026.8 1318663.8 CGMAT cycle number = 3 fast hessian tabulation Weight matrix 8.33123773E-02 Actual weight 10.000000 is applied to the X-ray term function value 1299075.1 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.015 0.019 Bond distances: others 814 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.914, B = -4.545 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.431, B = 13.631 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4601 Free R factor = 0.4661 Overall figure of merit = 0.4573 ----------------------------------------------------------------------------- Trying gamma equal 3.09090894E-02 Gamma decreased to 2.26446260E-02 fvalues 130022.21 5486.9697 1298305.5 1305709.1 CGMAT cycle number = 4 fast hessian tabulation Weight matrix 0.11380331 Actual weight 10.000000 is applied to the X-ray term function value 1292822.4 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.015 0.019 Bond distances: others 814 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.922, B = -2.505 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.433, B = 13.551 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4435 Free R factor = 0.4527 Overall figure of merit = 0.4908 ----------------------------------------------------------------------------- Trying gamma equal 2.26446260E-02 Gamma decreased to 1.51314782E-02 fvalues 129066.90 5778.6855 1290665.0 1296447.6 CGMAT cycle number = 5 fast hessian tabulation Weight matrix 0.15021561 Actual weight 10.000000 is applied to the X-ray term function value 1286953.0 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.016 0.019 Bond distances: others 814 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.925, B = -1.787 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.432, B = 13.319 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4291 Free R factor = 0.4402 Overall figure of merit = 0.5216 ----------------------------------------------------------------------------- Trying gamma equal 1.51314782E-02 Gamma decreased to 8.30134377E-03 fvalues 128389.23 5374.0273 1284402.1 1289266.4 CGMAT cycle number = 6 fast hessian tabulation Weight matrix 0.17622763 Actual weight 10.000000 is applied to the X-ray term function value 1281078.3 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.018 0.019 Bond distances: others 814 0.006 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.928, B = -1.509 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.432, B = 13.811 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4167 Free R factor = 0.4269 Overall figure of merit = 0.5404 ----------------------------------------------------------------------------- Trying gamma equal 8.30134377E-03 Gamma decreased to 2.09213095E-03 fvalues 127822.64 4993.6641 1278999.8 1283220.1 CGMAT cycle number = 7 fast hessian tabulation Weight matrix 0.20400964 Actual weight 10.000000 is applied to the X-ray term function value 1275760.0 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.019 0.019 Bond distances: others 814 0.005 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.930, B = -1.388 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.431, B = 15.221 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4057 Free R factor = 0.4143 Overall figure of merit = 0.5587 ----------------------------------------------------------------------------- Trying gamma equal 2.09213095E-03 Gamma decreased to 0.0000000 fvalues 127313.55 4722.1733 1274377.3 1277857.6 CGMAT cycle number = 8 fast hessian tabulation Weight matrix 0.23014112 Actual weight 10.000000 is applied to the X-ray term function value 1270635.1 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.020 0.019 Bond distances: others 814 0.004 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.933, B = -1.331 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.432, B = 15.539 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3961 Free R factor = 0.4060 Overall figure of merit = 0.5747 ----------------------------------------------------------------------------- Trying gamma equal 0.0000000 Trying gamma equal 2.56579034E-02 Gamma decreased to 2.05263235E-02 fvalues 126820.82 4668.4766 1270537.5 1272876.6 CGMAT cycle number = 9 fast hessian tabulation Weight matrix 0.22369781 Actual weight 9.0909090 is applied to the X-ray term function value 1152956.8 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.021 0.019 Bond distances: others 814 0.003 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.935, B = -1.263 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.432, B = 16.059 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3903 Free R factor = 0.4014 Overall figure of merit = 0.5831 ----------------------------------------------------------------------------- Trying gamma equal 2.05263235E-02 Gamma decreased to 1.58612505E-02 fvalues 126529.55 4654.6680 1153196.1 1154923.3 CGMAT cycle number = 10 fast hessian tabulation Weight matrix 0.21613531 Actual weight 8.2644625 is applied to the X-ray term function value 1046533.6 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.021 0.019 Bond distances: others 814 0.006 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.935, B = -1.232 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.431, B = 16.556 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.3857 Free R factor = 0.3983 Overall figure of merit = 0.5907 ----------------------------------------------------------------------------- Trying gamma equal 1.58612505E-02 Gamma decreased to 1.16202747E-02 fvalues 126285.92 4607.1719 1046891.1 1048292.4 **** Chiral volume outliers **** Chiral volume deviations from the ideal >10.000Sigma will be monitored A 56 LEU CG mod.= -0.31 id.= -2.59 dev= -2.278 sig.= 0.200 A 98 ILE CB mod.= -0.70 id.= 2.64 dev= 3.347 sig.= 0.200 A 124 ILE CB mod.= -0.32 id.= 2.64 dev= 2.969 sig.= 0.200 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\r11.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= 0.1040E+07 GEOM= 4472. TOTAL= 0.1045E+07 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 932 0.021 0.019 Bond distances: others 814 0.003 0.020 Bond angles : refined atoms 1255 2.478 1.916 Bond angles : others 1849 1.679 3.009 Torsion angles, period 1. refined 127 7.069 5.000 Torsion angles, period 2. refined 38 36.967 23.421 Torsion angles, period 3. refined 138 16.958 15.000 Torsion angles, period 3. others 8 7.108 15.000 Torsion angles, period 4. refined 7 24.879 15.000 Chiral centres: refined atoms 132 0.462 0.200 Planar groups: refined atoms 1106 0.012 0.020 Planar groups: others 217 0.002 0.020 VDW repulsions: refined_atoms 204 0.240 0.200 VDW repulsions.others 780 0.184 0.200 VDW; torsion: refined_atoms 455 0.188 0.200 VDW; torsion.others 534 0.105 0.200 HBOND: refined_atoms 10 0.060 0.200 VDW repulsions: symmetry: refined_atoms 15 0.306 0.200 VDW repulsions: symmetry: others 35 0.374 0.200 M. chain bond B values: refined atoms 513 0.200 0.221 M. chain bond B values: others 512 0.199 0.221 M. chain angle B values: refined atoms 638 0.337 0.329 M. chain angle B values: others 639 0.337 0.330 S. chain bond B values: refined atoms 418 0.402 0.247 S. chain bond B values: others 417 0.401 0.246 S. chain angle B values: refined atoms 616 0.600 0.364 S. chain angle B values: others 616 0.600 0.364 Long range B values: refined atoms 1042 0.790 1.813 Long range B values: others 1043 0.790 1.816 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.936, B = -1.205 Babinet"s bulk solvent: scale = 0.137, B = 120.183 Partial structure 1: scale = 0.430, B = 16.608 Overall anisotropic scale factors B11 = 0.13 B22 = 0.13 B33 = -0.27 B12 = 0.00 B13 = 0.00 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 21. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 21. v. resln :N:1,6,7,11,12: :Cycle 21. and v. resln :N:1,4,5,9,10: :Cycle 21. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.014 319 95.97 607.8 598.2 0.32 0.48 14 390.4 484.4 0.54 0.70 0.040 535 100.00 508.3 534.9 0.34 0.48 34 537.1 527.6 0.36 0.51 0.067 672 100.00 566.3 489.1 0.36 0.44 32 518.6 527.9 0.35 0.51 0.094 779 99.75 463.0 377.2 0.41 0.46 31 492.2 401.2 0.47 0.53 0.121 879 100.00 337.5 303.7 0.43 0.49 43 318.9 272.1 0.45 0.50 0.148 958 100.00 277.7 261.9 0.40 0.43 42 258.4 237.2 0.47 0.51 0.174 1040 100.00 258.1 236.0 0.38 0.40 38 275.0 277.2 0.33 0.38 0.201 1096 100.00 238.9 215.3 0.37 0.39 65 229.7 218.5 0.37 0.38 0.228 1185 100.00 215.9 193.1 0.36 0.37 56 227.3 200.6 0.32 0.32 0.255 1205 100.00 186.2 161.7 0.37 0.37 82 182.5 158.3 0.37 0.38 0.281 1298 100.00 159.6 139.8 0.40 0.39 59 153.9 130.5 0.38 0.37 0.308 1337 100.00 138.1 127.5 0.40 0.39 76 134.5 113.2 0.37 0.35 0.335 1403 100.00 124.1 112.6 0.39 0.37 88 118.1 110.7 0.44 0.39 0.362 1434 100.00 116.6 103.8 0.39 0.37 74 113.4 95.2 0.38 0.36 0.388 1507 100.00 108.6 94.2 0.37 0.35 76 104.0 99.8 0.41 0.38 0.415 1532 100.00 97.7 87.7 0.37 0.34 97 97.9 80.1 0.39 0.36 0.442 1579 100.00 91.9 81.6 0.37 0.35 92 93.2 79.9 0.38 0.36 0.469 1633 100.00 85.9 77.4 0.37 0.34 109 86.0 83.4 0.41 0.38 0.495 1576 93.50 74.5 70.6 0.43 0.39 79 77.7 74.0 0.42 0.37 0.522 1250 72.50 71.5 67.4 0.42 0.38 63 68.4 64.8 0.45 0.41 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 21. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 21. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0137 179 0.725 140 0.631 319 0.684 0.865 0.0405 376 0.706 159 0.620 535 0.681 0.832 0.0672 518 0.715 154 0.581 672 0.685 0.808 0.0940 623 0.599 156 0.528 779 0.585 0.788 0.1208 716 0.469 163 0.431 879 0.462 0.777 0.1475 800 0.541 158 0.431 958 0.523 0.801 0.1743 883 0.672 157 0.539 1040 0.652 0.847 0.2010 934 0.745 162 0.633 1096 0.728 0.912 0.2278 1022 0.718 163 0.617 1185 0.704 0.912 0.2546 1048 0.684 157 0.553 1205 0.667 0.901 0.2813 1136 0.625 162 0.520 1298 0.612 0.848 0.3081 1176 0.563 161 0.436 1337 0.548 0.762 0.3349 1243 0.566 160 0.464 1403 0.555 0.759 0.3616 1269 0.622 165 0.480 1434 0.605 0.813 0.3884 1347 0.651 160 0.548 1507 0.640 0.865 0.4151 1380 0.679 152 0.565 1532 0.668 0.861 0.4419 1421 0.673 158 0.567 1579 0.662 0.850 0.4687 1477 0.689 156 0.619 1633 0.683 0.861 0.4954 1447 0.380 131 0.268 1578 0.371 0.465 0.5222 1161 0.330 87 0.256 1248 0.325 0.429 $$ Resolution limits = 19.098 1.366 Number of used reflections = 23217 Percentage observed = 97.4781 Percentage of free reflections = 5.1089 Overall R factor = 0.3819 Free R factor = 0.3942 Overall weighted R factor = 0.3967 Free weighted R factor = 0.4092 Overall weighted R2 factor = 0.5072 Free weighted R2 factor = 0.5596 Overall correlation coefficient = 0.7963 Free correlation coefficient = 0.7549 Cruickshanks DPI for coordinate error= 0.1160 DPI based on free R factor = 0.1099 Overall figure of merit = 0.5957 ML based su of positional parameters = 0.1248 ML based su of thermal parameters = 6.7698 ----------------------------------------------------------------------------- Time in seconds: CPU = 0.00 Elapsed = 99.00 **** 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: $$ Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND zBOND rmsANGL zANGL rmsCHIRAL $$ $$ 0 0.5061 0.5138 0.374 132133. 7034.1 0.0 0.0 0.0 0.0 0.0 1 0.5046 0.5123 0.352 132089. 7030.7 0.0 0.0 0.0 0.0 0.0 2 0.5023 0.5085 0.350 131915. 7019.7 0.0 0.0 0.0 0.0 0.0 3 0.5009 0.5056 0.354 131709. 7007.2 0.0 0.0 0.0 0.0 0.0 4 0.5003 0.5037 0.357 131531. 6996.7 0.0 0.0 0.0 0.0 0.0 5 0.5000 0.5026 0.358 131386. 6988.3 0.0 0.0 0.0 0.0 0.0 6 0.4999 0.5017 0.358 131268. 6981.6 0.0 0.0 0.0 0.0 0.0 7 0.4999 0.5013 0.359 131182. 6976.6 0.0 0.0 0.0 0.0 0.0 8 0.4999 0.5009 0.359 131116. 6972.7 0.0 0.0 0.0 0.0 0.0 9 0.4998 0.5006 0.359 131060. 6969.5 0.0 0.0 0.0 0.0 0.0 10 0.4998 0.5005 0.359 131020. 6967.2 0.0301 1.655 2.137 1.240 0.690 11 0.4784 0.4807 0.410 130205. 6926.2 0.0180 0.985 1.672 0.864 0.612 12 0.4601 0.4661 0.457 129359. 6883.6 0.0145 0.761 1.678 0.814 0.558 13 0.4435 0.4527 0.491 128704. 6849.9 0.0149 0.757 1.813 0.867 0.522 14 0.4291 0.4402 0.522 128158. 6825.3 0.0162 0.816 1.966 0.940 0.497 15 0.4167 0.4269 0.540 127608. 6801.4 0.0178 0.892 2.116 1.017 0.482 16 0.4057 0.4143 0.559 127104. 6781.0 0.0191 0.957 2.240 1.083 0.473 17 0.3961 0.4060 0.575 126597. 6761.9 0.0202 1.011 2.348 1.141 0.469 18 0.3903 0.4014 0.583 126313. 6752.5 0.0212 1.056 2.432 1.184 0.468 19 0.3857 0.3983 0.591 126073. 6745.0 0.0214 1.066 2.472 1.202 0.466 20 0.3819 0.3942 0.596 125866. 6737.6 0.0212 1.051 2.478 1.200 0.462 $$ $TEXT:Result: $$ Final results $$ Initial Final R factor 0.5061 0.3819 R free 0.5138 0.3942 Rms BondLength 0.0301 0.0212 Rms BondAngle 2.1372 2.4784 Rms ChirVolume 0.6904 0.4615 $$
Refmac_5.7.0032: End of Refmac_5.7.0032 Times: User: 0.0s System: 0.0s Elapsed: 1:51
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CCP4i: Writing final coordinates (XYZOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r11.pdb
CCP4i: Writing final phases (HKLOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r11.mtz
CCP4i: Writing final TLS (TLSOUT) to C:/SOLVE_REFINE/lizozim/mr-refine-build/r11.tls
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