############################################################### ############################################################### ############################################################### ### CCP4 7.0.078: Refmac version 5.8.0258 : 09/10/19## ############################################################### User: maly Run date: 26/ 5/2020 Run time: 14:26:43 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 41.96 1.90 resi MLKF meth CGMAT bref MIXED Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES Data line--- bins 4 Data line--- ncyc 10 Data line--- monitor MEDIum Data line--- free 3 Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: CDO_R.mtz LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - CDO_complete_R03_2-00A.pdb Output coordinate file. Logical name - XYZOUT actual file name - CDO_complete_R03_1-90A.pdb Input reflection file. Logical name - HKLIN actual file name - CDO_R.mtz Output reflection file. Logical name - HKLOUT actual file name - CDO_complete_R03_1-90A.mtz Cell from mtz : 57.632 57.632 122.391 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 : /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: 4 0.0693 Refinement of mixed isotropic and anisotropic Bfactors Refinement resln : 41.9635 1.9000 Estimated number of reflections : 21862 Free R exclusion - flag equals: 3 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: 41.9635 1.9000 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 :CDO_complete_R03_2-00A.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 : 1836 Number of residues : 502 Number of chains : 4 I am reading library. Please wait. mon_lib.cif INFO: link is found (not be used) dist= 2.026 ideal_dist= 2.090 ch:AAA res: 86 HIS at:NE2 .->ch:AaA res: 501 FE at:FE . INFO: link is found (not be used) dist= 2.233 ideal_dist= 2.090 ch:AAA res: 88 HIS at:NE2 .->ch:AaA res: 501 FE at:FE . INFO: link is found (not be used) dist= 1.826 ideal_dist= 1.720 ch:AAA res: 93 CYS at:SG .->ch:AAA res: 157 TYR at:CE1 . INFO: link is found (not be used) dist= 2.233 ideal_dist= 2.090 ch:AAA res: 140 HIS at:NE2 .->ch:AaA res: 501 FE at:FE . INFO: link is found (not be used) dist= 2.333 ideal_dist= 1.945 ch:AaA res: 501 FE at:FE .->ch:AbA res: 901 2CO at:N . INFO: link is found (not be used) dist= 2.433 ideal_dist= 2.235 ch:AaA res: 501 FE at:FE .->ch:AbA res: 901 2CO at:SG . INFO: link is found (not be used) dist= 2.043 ideal_dist= 1.870 ch:AaA res: 501 FE at:FE .->ch:AbA res: 901 2CO at:OD . -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:26-MAY-20 -------------------------------- ATTENTION: atom:OXT THR 171 AAA is missing in the structure ATTENTION: atom:OXT PRO 190 AAA is missing in the structure Number of chains : 4 Total number of monomers : 502 Number of atoms : 3948 Number of missing atoms : 0 Number of rebuilt atoms : 1482 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 1.0490 FE 11.7738 4.7611 7.3600 0.3072 3.5235 15.3535 2.3054 76.8805 1.2805 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: 2950 0 2950 Angles: 5345 0 5345 Chirals: 196 0 196 Planes: 451 0 451 Torsions: 1553 0 1553 Intervals: 0 0 0 -------------------------------------------------------------------------------- Number of harmonic restraints = 0 Number of atoms in special position = 0 ----------------------------------------------------- **** Info from mtz file **** FreeR flag 3 Number of "free" reflections 803 Number of all reflections 16986 -------------------------------------------------------------------------------- Number of reflections in file 39842 Number of reflections read 16986 Current auto weighting coefficient = 7.2495699 mode : HKRF ###### TLS Group Definitions ###### CGMAT cycle number = 1 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored A 125 LEU C . - A 126 ARG N . mod.= 1.524 id.= 1.337 dev= -0.187 sig.= 0.011 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 93 CYS SG . - A 157 TYR HE1 . mod.= 0.892 id.= 3.000 dev= -2.11 sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 Limits of asymmetric unit : 1.00 1.00 0.13 Grid spacing to be used : 112 112 240 Maximuum H,K,L : 31 31 65 Minimum acceptable grid spacing: 73 73 154 Limits of asymmetric unit : 1.00 1.00 0.13 Grid spacing to be used : 112 112 240 Maximuum H,K,L : 31 31 65 Minimum acceptable grid spacing: 73 73 154 Weight matrix 0.26080608 Actual weight 7.2495699 is applied to the X-ray term Norm of X_ray positional gradient 41.5 Norm of Geom. positional gradient 87.6 Norm of X_ray B-factor gradient 137. Norm of Geom. B-factor gradient 0.217E+05 Product of X_ray and Geom posit. gradients -0.944E+07 Cosine of angle between them -0.268 Product of X_ray and Geom B-fact gradients -0.435E+08 Cosine of angle between them -0.005 Residuals: XRAY= 0.6373E+06 GEOM= 0.2692E+05 TOTAL= 0.6642E+06 function value 664231.81 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 1557 0.014 0.013 Bond distances: others 1393 0.035 0.017 Bond angles : refined atoms 2103 1.885 1.644 Bond angles : others 3242 2.364 1.582 Torsion angles, period 1. refined 184 7.263 5.000 Torsion angles, period 2. refined 90 37.012 22.778 Torsion angles, period 3. refined 268 14.637 15.000 Torsion angles, period 4. refined 9 12.118 15.000 Chiral centres: refined atoms 196 0.088 0.200 Planar groups: refined atoms 1736 0.013 0.020 Planar groups: others 331 0.016 0.020 VDW repulsions: refined_atoms 322 0.255 0.200 VDW repulsions.others 1348 0.231 0.200 VDW; torsion: refined_atoms 711 0.171 0.200 VDW; torsion.others 700 0.081 0.200 HBOND: refined_atoms 225 0.218 0.200 HBOND.others 4 0.065 0.200 VDW repulsions: symmetry: refined_atoms 11 0.227 0.200 VDW repulsions: symmetry: others 31 0.161 0.200 HBOND: symmetry: refined_atoms 17 0.230 0.200 HBOND: symmetry: others 1 0.094 0.200 M. chain bond B values: refined atoms 745 1.559 1.169 M. chain bond B values: others 745 1.558 1.169 M. chain angle B values: refined atoms 926 2.507 1.734 M. chain angle B values: others 927 2.506 1.734 S. chain bond B values: refined atoms 811 2.612 1.520 S. chain bond B values: others 810 2.607 1.519 S. chain angle B values: refined atoms 1177 4.137 2.128 S. chain angle B values: others 1178 4.135 2.127 Long range B values: refined atoms 1863 6.862 16.525 Long range B values: others 1768 6.528 15.218 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall scale should be multiplied by 1.0000 Overall : scale = 0.0402, B = 0.3529 Partial structure 1: scale = 0.3734, B = 49.0003 Overall anisotropic scale factors B11 = -0.27 B22 = -0.27 B33 = 0.54 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.