############################################################### ############################################################### ############################################################### ### CCP4 7.0.078: Refmac version 5.8.0258 : 09/10/19## ############################################################### User: maly Run date: 26/ 5/2020 Run time: 13:57:37 Please reference: Collaborative Computational Project, Number 4. 2011. "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242. as well as any specific reference in the program write-up.$TEXT:Reference1: $$ Primary reference $$ "Overview of refinement procedures within REFMAC5: utilizing data from different sources" O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) Acta Crystallogr. D74, 492-505 $$ $SUMMARY :Reference1: $$ Refmac: $$ :TEXT:Reference1: $$ $TEXT:Reference1: $$ Primary reference for EM $$ "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) Acta Crystallogr. D74, 215-227 $$ $SUMMARY :Reference2: $$ Refmac: $$ :TEXT:Reference1: $$ $TEXT:Reference1: $$ Secondary reference $$ "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 $$ $SUMMARY :Reference3: $$ 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 $$ $SUMMARY :Reference4: $$ Refmac: $$ :TEXT:Reference2: $$ Data line--- make check NONE Data line--- refi type REST reso 79.98 1.70 resi MLKF meth CGMAT bref MIXED Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES Data line--- bins 7 Data line--- ncyc 10 Data line--- monitor MEDIum Data line--- free 0 Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: AUTOMATIC_DEFAULT_free_R.mtz LABIN FP=F SIGFP=SIGF FREE=FreeR_flag **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - TL_step0-01A_R00_1-71A.pdb Output coordinate file. Logical name - XYZOUT actual file name - TL_step0-01A_R00_1-70A.pdb Input reflection file. Logical name - HKLIN actual file name - AUTOMATIC_DEFAULT_free_R.mtz Output reflection file. Logical name - HKLOUT actual file name - TL_step0-01A_R00_1-70A.mtz Cell from mtz : 92.354 92.354 127.712 90.000 90.000 120.000 Space group from mtz: number - 178; name - P 61 2 2 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/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 Standard sugar links 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 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: 7 0.0494 Refinement of mixed isotropic and anisotropic Bfactors Refinement resln : 79.9808 1.7000 Estimated number of reflections : 53643 Free R exclusion - flag equals: 0 Auto weighting. An attempt Refinement cycles : 10 Scaling type : Wilson scaling type with Guassians 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: 79.9808 1.7000 Damping factors: 1.0000 1.0000 1.0000 **** Geometry restraints and weights **** Sigma: Bonding distances Weight = 1.00 Bond angles Weight = 1.00 Planar groups (all and main chain) WEIGHT= 1.00 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 Rigid bond outliers 10.000 Sphericity outliers 10.000 --------------------------------------------------------------- Input file :TL_step0-01A_R00_1-71A.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 5.51 _lib_update 11/07/18 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 24624 with complete description : 24624 NUMBER OF MODIFICATIONS : 70 NUMBER OF LINKS : 77 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) Number of atoms : 2816 Number of residues : 691 Number of chains : 15 I am reading library. Please wait. mon_lib.cif INFO: link is found (not be used) dist= 2.364 ideal_dist= 2.320 ch:AAA res: 57 ASP at:OD1 .->ch:AdA res: 503 CA at:CA . INFO: link is found (not be used) dist= 2.584 ideal_dist= 2.320 ch:AAA res: 57 ASP at:OD2 .->ch:AdA res: 503 CA at:CA . INFO: link is found (not be used) dist= 2.427 ideal_dist= 2.320 ch:AAA res: 59 ASP at:OD1 .->ch:AdA res: 503 CA at:CA . INFO: link is found (not be used) dist= 2.323 ideal_dist= 2.320 ch:AAA res: 61 GLN at:O .->ch:AdA res: 503 CA at:CA . INFO: link is found (not be used) dist= 2.370 ideal_dist= 2.320 ch:AAA res: 138 ASP at:OD2 .->ch:AbA res: 501 CA at:CA . INFO: link is found (not be used) dist= 2.006 ideal_dist= 2.058 ch:AAA res: 142 HIS at:NE2 .->ch:AaA res: 401 ZN at:ZN . INFO: link is found (not be used) dist= 2.033 ideal_dist= 2.058 ch:AAA res: 146 HIS at:NE2 .->ch:AaA res: 401 ZN at:ZN . INFO: link is found (not be used) dist= 1.931 ideal_dist= 2.055 ch:AAA res: 166 GLU at:OE1 .->ch:AaA res: 401 ZN at:ZN . INFO: link is found (not be used) dist= 2.453 ideal_dist= 2.320 ch:AAA res: 177 GLU at:OE1 .->ch:AbA res: 501 CA at:CA . INFO: link is found (not be used) dist= 2.560 ideal_dist= 2.320 ch:AAA res: 177 GLU at:OE2 .->ch:AbA res: 501 CA at:CA . INFO: link is found (not be used) dist= 2.775 ideal_dist= 2.320 ch:AAA res: 183 ASN at:O .->ch:AcA res: 502 CA at:CA . INFO: link is found (not be used) dist= 2.433 ideal_dist= 2.320 ch:AAA res: 185 ASP at:OD1 .->ch:AbA res: 501 CA at:CA . INFO: link is found (not be used) dist= 2.390 ideal_dist= 2.320 ch:AAA res: 187 GLU at:O .->ch:AbA res: 501 CA at:CA . INFO: link is found (not be used) dist= 2.611 ideal_dist= 2.320 ch:AAA res: 190 GLU at:OE1 .->ch:AbA res: 501 CA at:CA . INFO: link is found (not be used) dist= 2.425 ideal_dist= 2.320 ch:AAA res: 190 GLU at:OE2 .->ch:AbA res: 501 CA at:CA . INFO: link is found (not be used) dist= 2.644 ideal_dist= 2.320 ch:AAA res: 190 GLU at:OE2 .->ch:AcA res: 502 CA at:CA . INFO: link is found (not be used) dist= 2.346 ideal_dist= 2.320 ch:AAA res: 193 TYR at:O .->ch:AeA res: 504 CA at:CA . INFO: link is found (not be used) dist= 2.404 ideal_dist= 2.320 ch:AAA res: 194 THR at:OG1 .->ch:AeA res: 504 CA at:CA . INFO: link is found (not be used) dist= 2.365 ideal_dist= 2.320 ch:AAA res: 194 THR at:O .->ch:AeA res: 504 CA at:CA . INFO: link is found (not be used) dist= 2.308 ideal_dist= 2.320 ch:AAA res: 197 ILE at:O .->ch:AeA res: 504 CA at:CA . INFO: link is found (not be used) dist= 2.338 ideal_dist= 2.320 ch:AAA res: 200 ASP at:OD1 .->ch:AeA res: 504 CA at:CA . -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:09-OCT-19 -------------------------------- ATTENTION: atom:CG GLN 128 AAA is missing in the structure ATTENTION: atom:CD GLN 128 AAA is missing in the structure ATTENTION: atom:OE1 GLN 128 AAA is missing in the structure ATTENTION: atom:NE2 GLN 128 AAA is missing in the structure ATTENTION: atom:CG LYS 182 AAA is missing in the structure ATTENTION: atom:CD LYS 182 AAA is missing in the structure ATTENTION: atom:CE LYS 182 AAA is missing in the structure ATTENTION: atom:NZ LYS 182 AAA is missing in the structure ATTENTION: atom:CG GLN 225 AAA is missing in the structure ATTENTION: atom:CD GLN 225 AAA is missing in the structure ATTENTION: atom:OE1 GLN 225 AAA is missing in the structure ATTENTION: atom:NE2 GLN 225 AAA is missing in the structure ATTENTION: atom:CG LYS 316 AAA is missing in the structure ATTENTION: atom:CD LYS 316 AAA is missing in the structure ATTENTION: atom:CE LYS 316 AAA is missing in the structure ATTENTION: atom:NZ LYS 316 AAA is missing in the structure Number of chains : 15 Total number of monomers : 691 Number of atoms : 5886 Number of missing atoms : 16 Number of rebuilt atoms : 2298 Number of unknown atoms : 0 Number of deleted atoms : 0 _ccp4_form_factor.scat_method 'Sum of Gaussians' _ccp4_form_factor.scat_data_source X-ray 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 12.2220 0.0057 3.1346 9.8933 2.0141 28.9975 1.1672 0.5826 -11.5379 H 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7997 0.0030 C 2.3103 20.8439 1.0201 10.2075 1.5888 0.5687 0.8651 51.6512 0.2156 O 3.0487 13.2771 2.2870 5.7011 1.5464 0.3239 0.8671 32.9089 0.2508 S 6.9054 1.4679 5.2035 22.2151 1.4379 0.2536 1.5863 56.1720 1.1154 ZN 14.0824 3.2655 7.0359 0.2333 5.1655 10.3163 2.4114 58.7097 -1.0360 CA 8.6266 10.4421 7.3873 0.6599 1.5899 85.7484 1.0211 178.4370 1.7233 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: 4636 0 4636 Angles: 8341 0 8341 Chirals: 326 0 326 Planes: 758 0 758 Torsions: 2521 0 2521 Intervals: 0 0 0 -------------------------------------------------------------------------------- Number of harmonic restraints = 0 Number of atoms in special position = 0 ----------------------------------------------------- **** Info from mtz file **** FreeR flag 0 Number of "free" reflections 1831 Number of all reflections 36034 -------------------------------------------------------------------------------- Number of reflections in file 76614 Number of reflections read 36034 Current auto weighting coefficient = 6.7495689 mode : HKRF ###### TLS Group Definitions ###### CGMAT cycle number = 1 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 120 MET CG - A 120 MET CE mod.= 83.46 id.= 100.60 dev= 17.135 sig.= 1.500 Limits of asymmetric unit : 1.00 1.00 0.08 Grid spacing to be used : 192 192 264 Maximuum H,K,L : 55 55 76 Minimum acceptable grid spacing: 126 126 174 Limits of asymmetric unit : 1.00 1.00 0.08 Grid spacing to be used : 192 192 264 Maximuum H,K,L : 55 55 76 Minimum acceptable grid spacing: 126 126 174 Weight matrix 0.32992744 Actual weight 6.7495689 is applied to the X-ray term Norm of X_ray positional gradient 41.6 Norm of Geom. positional gradient 86.6 Norm of X_ray B-factor gradient 70.9 Norm of Geom. B-factor gradient 63.0 Product of X_ray and Geom posit. gradients -0.258E+08 Cosine of angle between them -0.481 Product of X_ray and Geom B-fact gradients -0.189E+08 Cosine of angle between them -0.854 Residuals: XRAY= 0.1176E+07 GEOM= 0.1797E+05 TOTAL= 0.1194E+07 function value 1194115.9 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 2501 0.012 0.013 Bond distances: others 2135 0.038 0.017 Bond angles : refined atoms 3405 1.698 1.643 Bond angles : others 4936 2.468 1.576 Torsion angles, period 1. refined 316 6.242 5.000 Torsion angles, period 2. refined 132 29.898 23.258 Torsion angles, period 3. refined 350 13.395 15.000 Torsion angles, period 4. refined 10 16.841 15.000 Chiral centres: refined atoms 326 0.084 0.200 Planar groups: refined atoms 2920 0.010 0.020 Planar groups: others 554 0.014 0.020 VDW repulsions: refined_atoms 577 0.239 0.200 VDW repulsions.others 2085 0.221 0.200 VDW; torsion: refined_atoms 1306 0.178 0.200 VDW; torsion.others 1008 0.076 0.200 HBOND: refined_atoms 233 0.179 0.200 HBOND.others 1 0.054 0.200 Metal-ion: refined_atoms 16 0.069 0.200 VDW repulsions: symmetry: refined_atoms 17 0.299 0.200 VDW repulsions: symmetry: others 43 0.264 0.200 HBOND: symmetry: refined_atoms 22 0.277 0.200 M. chain bond B values: refined atoms 1270 1.819 2.256 M. chain bond B values: others 1269 1.819 2.255 M. chain angle B values: refined atoms 1584 2.284 3.380 M. chain angle B values: others 1585 2.284 3.381 S. chain bond B values: refined atoms 1231 2.695 2.480 S. chain bond B values: others 1231 2.694 2.482 S. chain angle B values: refined atoms 1821 3.756 3.630 S. chain angle B values: others 1821 3.756 3.631 Long range B values: refined atoms 3096 4.940 28.595 Long range B values: others 3097 4.940 28.605 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall scale should be multiplied by 1.0000 Overall : scale = 1.0559, B = -0.0277 Partial structure 1: scale = 0.4208, B = 51.2720 Overall anisotropic scale factors B11 = -0.28 B22 = -0.28 B33 = 0.91 B12 = -0.14 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.