############################################################### ############################################################### ############################################################### ### CCP4 8.0.007: Refmac version 5.8.0403 : 11/30/22## ############################################################### User: unknown Run date: 21/12/2022 Run time: 13:04:27 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 47.32 2.10 resi MLKF meth CGMAT bref MIXED Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES Data line--- bins 5 Data line--- ncyc 10 Data line--- weight matrix 0.0600 Data line--- monitor MEDIum Data line--- free 0 Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: poli67_1-9A.mtz LABIN FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - poli_ccp4sw2023_R00_2-30A.pdb Output coordinate file. Logical name - XYZOUT actual file name - poli_ccp4sw2023_R00_2-10A.pdb Input reflection file. Logical name - HKLIN actual file name - poli67_1-9A.mtz Output reflection file. Logical name - HKLOUT actual file name - poli_ccp4sw2023_R00_2-10A.mtz Cell from mtz : 58.265 79.758 94.643 90.000 90.000 90.000 Space group from mtz: number - 19; name - P 21 21 21 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /opt/ccp4/ccp4-8.0/lib/data/monomers/mon*cif Parameters for neW entry and VDW: /opt/ccp4/ccp4-8.0/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: 5 0.0454 Refinement of mixed isotropic and anisotropic Bfactors Refinement resln : 47.3245 2.1000 Estimated number of reflections : 34260 Free R exclusion - flag equals: 0 Weighting by comparison of trace of matrix Weighting parameters : 0.0600 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: 47.3245 2.1000 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 :poli_ccp4sw2023_R00_2-30A.pdb NUMBER OF MONOMERS IN THE LIBRARY : 35279 with complete description : 35279 NUMBER OF MODIFICATIONS : 119 NUMBER OF LINKS : 98 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) set_mod Number of atoms : 2286 Number of residues : 307 Number of chains : 3 --------- I am reading library. Please wait. mon_lib.cif ******Default connectivity******* **** Automatic generation of links **** Link info given in this sectoion is for information only If you want to use this links then either add them into the pdb/mmcif file or use make link yes option In create description -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:24-OCT-17 -------------------------------- ATTENTION: atom:OXT ASN 69 A1_ is missing in the structure ATTENTION: atom:OXT ARG 164 A1_ is missing in the structure ATTENTION: atom:OXT PRO 36 B2_ is missing in the structure ATTENTION: atom:OXT THR 70 B2_ is missing in the structure ATTENTION: atom:OXT ASN 153 B2_ is missing in the structure Number of chains : 3 Total number of monomers : 307 Number of atoms : 4696 Number of missing atoms : 5 Number of rebuilt atoms : 2331 Number of unknown atoms : 0 Number of deleted atoms : 0 In create description -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:24-OCT-17 -------------------------------- ATTENTION: atom:OXT ASN 69 A1_ is missing in the structure ATTENTION: atom:OXT ARG 164 A1_ is missing in the structure ATTENTION: atom:OXT PRO 36 B2_ is missing in the structure ATTENTION: atom:OXT THR 70 B2_ is missing in the structure ATTENTION: atom:OXT ASN 153 B2_ is missing in the structure Number of chains : 3 Total number of monomers : 307 Number of atoms : 4696 Number of missing atoms : 5 Number of rebuilt atoms : 0 Number of unknown atoms : 0 Number of deleted atoms : 0 Number of bonds restraints : 4571 Number of angles restraints : 8304 Number of torsions restraints : 2161 Number of chiralities : 329 Number of planar groups : 746 Scattering factors file : /opt/ccp4/ccp4-8.0/lib/data/atomsf.lib _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 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 H 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7997 0.0030 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: 4571 0 4571 Angles: 8304 0 8304 Chirals: 329 0 329 Planes: 746 0 746 Torsions: 2161 0 2161 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 1283 Number of all reflections 26407 -------------------------------------------------------------------------------- Number of reflections in file 35470 Number of reflections read 26407 Current auto weighting coefficient = 7.74955940 ###### TLS Group Definitions ###### CGMAT cycle number = 1 Limits of asymmetric unit : 1.00 1.00 0.25 Grid spacing to be used : 108 144 168 Maximuum H,K,L : 28 39 46 Minimum acceptable grid spacing: 68 94 111 Limits of asymmetric unit : 1.00 1.00 0.25 Grid spacing to be used : 108 144 168 Maximuum H,K,L : 28 39 46 Minimum acceptable grid spacing: 68 94 111 Weight matrix 5.99999987E-02 Actual weight 23.8534813 is applied to the X-ray term Norm of X_ray positional gradient 40.1 Norm of Geom. positional gradient 85.2 Norm of X_ray B-factor gradient 47.1 Norm of Geom. B-factor gradient 24.0 Product of X_ray and Geom posit. gradients -0.156E+08 Cosine of angle between them -0.333 Product of X_ray and Geom B-fact gradients -0.359E+07 Cosine of angle between them -0.693 Residuals: XRAY= 0.2527E+07 GEOM= 0.1252E+05 TOTAL= 0.2540E+07 function value 2540014.25 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 2284 0.017 0.012 Bond distances: others 2287 0.002 0.016 Bond angles : refined atoms 3054 1.858 1.652 Bond angles : others 5250 0.896 1.577 Torsion angles, period 1. refined 265 7.195 5.000 Torsion angles, period 2. refined 19 1.538 5.000 Torsion angles, period 3. refined 475 21.320 10.000 Torsion angles, period 6. refined 116 16.895 10.000 Chiral centres: refined atoms 329 0.077 0.200 Planar groups: refined atoms 2643 0.009 0.020 Planar groups: others 553 0.011 0.020 VDW repulsions: refined_atoms 507 0.222 0.200 VDW repulsions.others 1922 0.211 0.200 VDW; torsion: refined_atoms 1091 0.171 0.200 VDW; torsion.others 1236 0.079 0.200 HBOND: refined_atoms 50 0.175 0.200 VDW repulsions: symmetry: refined_atoms 10 0.147 0.200 VDW repulsions: symmetry: others 30 0.268 0.200 HBOND: symmetry: refined_atoms 3 0.135 0.200 M. chain bond B values: refined atoms 1075 7.318 7.057 M. chain bond B values: others 1075 7.298 7.056 M. chain angle B values: refined atoms 1335 9.833 12.701 M. chain angle B values: others 1336 9.833 12.709 S. chain bond B values: refined atoms 1209 8.646 7.896 S. chain bond B values: others 1210 8.642 7.899 S. chain angle B values: refined atoms 1719 12.333 14.170 S. chain angle B values: others 1720 12.329 14.173 Long range B values: refined atoms 2586 14.521 67.752 Long range B values: others 2586 14.533 67.770 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall scale should be multiplied by 1.0000 Overall : scale = 1.5332, B = 0.1974 Partial structure 1: scale = 0.3834, B = 54.3986 Overall anisotropic scale factors B11 = 5.60 B22 = -1.82 B33 = -3.78 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.