############################################################### ############################################################### ############################################################### ### CCP4 7.0.078: Refmac version 5.8.0258 : 09/10/19## ############################################################### User: maly Run date: 26/ 5/2020 Run time: 12:00:58 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 42.68 1.15 resi MLKF meth CGMAT bref MIXED Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES Data line--- bins 11 Data line--- ncyc 10 Data line--- monitor MEDIum Data line--- free 0 Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: EP_R.mtz LABIN FP=FP SIGFP=SIGFP FREE=FREE **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - EP_R00_1-20A.pdb Output coordinate file. Logical name - XYZOUT actual file name - EP_R00_1-15A.pdb Input reflection file. Logical name - HKLIN actual file name - EP_R.mtz Output reflection file. Logical name - HKLOUT actual file name - EP_R00_1-15A.mtz Cell from mtz : 45.203 73.097 52.573 90.000 109.248 90.000 Space group from mtz: number - 4; name - P 1 21 1 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: 11 0.0687 Refinement of mixed isotropic and anisotropic Bfactors Refinement resln : 42.6836 1.1500 Estimated number of reflections : 164864 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: 42.6836 1.1500 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 :EP_R00_1-20A.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 : 2459 Number of residues : 330 Number of chains : 1 I am reading library. Please wait. mon_lib.cif -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:26-MAY-20 -------------------------------- ATTENTION: atom:CE LYS 63 AAA is missing in the structure ATTENTION: atom:NZ LYS 63 AAA is missing in the structure ATTENTION: atom:CD LYS 68 AAA is missing in the structure ATTENTION: atom:CE LYS 68 AAA is missing in the structure ATTENTION: atom:NZ LYS 68 AAA is missing in the structure ATTENTION: atom:CE LYS 110 AAA is missing in the structure ATTENTION: atom:NZ LYS 110 AAA is missing in the structure ATTENTION: atom:NZ LYS 142 AAA is missing in the structure ATTENTION: atom:NZ LYS 149 AAA is missing in the structure ATTENTION: atom:CG LYS 191 AAA is missing in the structure ATTENTION: atom:CD LYS 191 AAA is missing in the structure ATTENTION: atom:CE LYS 191 AAA is missing in the structure ATTENTION: atom:NZ LYS 191 AAA is missing in the structure ATTENTION: atom:NZ LYS 243 AAA is missing in the structure ATTENTION: atom:OXT ALA 328 AAA is missing in the structure Number of chains : 1 Total number of monomers : 330 Number of atoms : 4853 Number of missing atoms : 7 Number of rebuilt atoms : 2344 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 1.0317 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: 4719 0 4719 Angles: 8613 0 8613 Chirals: 376 0 376 Planes: 786 0 786 Torsions: 2619 0 2619 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 5767 Number of all reflections 114320 -------------------------------------------------------------------------------- Number of reflections in file 149916 Number of reflections read 114320 Current auto weighting coefficient = 5.3747091 mode : HKRF ###### TLS Group Definitions ###### CGMAT cycle number = 1 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 328 ALA C . - A 329 SER H B mod.= 0.892 id.= 2.950 dev= -2.06 sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 128 210 150 Maximuum H,K,L : 40 64 46 Minimum acceptable grid spacing: 85 137 99 Limits of asymmetric unit : 1.00 1.00 0.50 Grid spacing to be used : 128 210 150 Maximuum H,K,L : 40 64 46 Minimum acceptable grid spacing: 85 137 99 Weight matrix 0.22189483 Actual weight 5.3747091 is applied to the X-ray term Norm of X_ray positional gradient 73.7 Norm of Geom. positional gradient 98.9 Norm of X_ray B-factor gradient 117. Norm of Geom. B-factor gradient 0.161E+04 Product of X_ray and Geom posit. gradients -0.504E+08 Cosine of angle between them -0.496 Product of X_ray and Geom B-fact gradients -0.206E+08 Cosine of angle between them -0.006 Residuals: XRAY= 0.2374E+07 GEOM= 0.2330E+05 TOTAL= 0.2397E+07 function value 2397374.5 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 2533 0.014 0.013 Bond distances: others 2186 0.038 0.017 Bond angles : refined atoms 3498 1.793 1.637 Bond angles : others 5115 2.544 1.563 Torsion angles, period 1. refined 363 6.970 5.000 Torsion angles, period 2. refined 86 29.764 25.000 Torsion angles, period 3. refined 342 10.454 15.000 Torsion angles, period 4. refined 1 14.939 15.000 Chiral centres: refined atoms 376 0.090 0.200 Planar groups: refined atoms 2955 0.013 0.020 Planar groups: others 524 0.024 0.020 VDW repulsions: refined_atoms 432 0.240 0.200 VDW repulsions.others 1916 0.228 0.200 VDW; torsion: refined_atoms 1289 0.173 0.200 VDW; torsion.others 1073 0.079 0.200 HBOND: refined_atoms 36 0.124 0.200 VDW repulsions: symmetry: refined_atoms 2 0.082 0.200 VDW repulsions: symmetry: others 26 0.145 0.200 HBOND: symmetry: refined_atoms 3 0.022 0.200 M. chain bond B values: refined atoms 1369 1.770 1.317 M. chain bond B values: others 1368 1.772 8292.663 M. chain angle B values: refined atoms 1719 2.065 1.995 M. chain angle B values: others 1720 2.065 11.002 S. chain bond B values: refined atoms 1164 2.229 1.438 S. chain bond B values: others 1164 2.229********** S. chain angle B values: refined atoms 1765 2.501 2.103 S. chain angle B values: others 1765 2.501 2.102 Long range B values: refined atoms 2679 2.493 15.895 Long range B values: others 2680 2.493 20.511 Rigid bond restraints 2533 7.613 3.000 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall scale should be multiplied by 1.0000 Overall : scale = 0.0485, B = -0.4714 Partial structure 1: scale = 0.5067, B = 39.4322 Overall anisotropic scale factors B11 = 1.15 B22 = -0.03 B33 = -0.25 B12 = 0.00 B13 = -1.16 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 1. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 1.