############################################################### ############################################################### ############################################################### ### CCP4 9.0.002: Refmac version 5.8.0430 : 05/20/24## ############################################################### User: afonine Run date: 12/ 8/2024 Run time: 12:49:51 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--- labin FP=Fout PHIB=Pout Data line--- make hydr all Data line--- make hout no Data line--- solvent no Data line--- scale lssc isot Data line--- source em mb Data line--- ncycle 10 Data line--- reso 3.0 Data line--- weight auto 1.96e+00 Data line--- ncsr local Data line--- pdbo keep auth Data line--- make cr prepared Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: masked_fs_obs.mtz ===> Warning: Figure of merit of phases has not been assigned ===> Warning: They will be assumed to be equal to 1.0 If coordinates and restraints have been prepared by an external program then "make hydr yes" is assumed Hydrogen atoms will be read and used **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - shifted.crd Output coordinate file. Logical name - XYZOUT actual file name - shifted_refined.pdb Input reflection file. Logical name - HKLIN actual file name - masked_fs_obs.mtz Output reflection file. Logical name - HKLOUT actual file name - shifted_refined.mtz Cell from mtz : 125.400 66.000 96.800 90.000 90.000 90.000 Space group from mtz: number - 1; name - P 1 Refinement type : Restrained **** Makecif parameters **** Parameters for VDW and ion radii: /net/anaconda/raid1/afonine/work/CCP4/ccp4-9/lib/data/monomers/ener_lib.cif Residual : Phase modified Maximum Likelihood for Fs Phase Blurred by Scale*Exp(-B s**2) : 1.00 0.00 **** Least-square scaling parameters **** Overall scale Overall B value **** 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 0.0056 Refinement of individual isotropic Bfactors Refinement resln : 125.4000 3.0000 Estimated number of reflections : 89258 Auto weighting. An attempt Refinement cycles : 10 Scaling type : Wilson scaling type with Guassians Estimation of D/Sigma in resolution bins using working set of reflns with experimental sigmas Input phases not used in SigmaA estimation Scaling and SigmaA resln: 125.4000 3.0000 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 NCS will defined automatically and applied **** Alignment parameters **** Alignment leve 80.000% Aligment cut 2.000A Iterative aligment N **** Local NCS parameters **** Maximum distance 4.2000A Maximum difference of distances 1.0000A Geman-Mcclure parameter 0.1000 Weights sigx = 0.0500 if dist1+dist2<8.0 sigx = 0.0500*sqrt((dist1+dist2)/8.0) if dist1+dist2>=8.0 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 --------------------------------------------------------------- ------------------------------------------ Number of chains : 4 Number of monomers : 332 Number of atoms : 5092 ------------------------------------------ ********* Alignment results ********* ----------------------------------------------------------------------------------------------------------------------- : Ncsr group : Chain 1 : Chain 2 : No of aligned : Score : RMS : Ave(RmsLoc) : ----------------------------------------------------------------------------------------------------------------------- : 1 : 0_p ( 158 - 202 ) : 1_p ( 158 - 202 ) : 45 : 1.0000 : 2.9307 : 1.4485 : ----------------------------------------------------------------------------------------------------------------------- -------------------------------------------------------------------------------- **** Assign all residues to one of the chains **** -------------------------------------------------------------------------------- The program will use local ncs restraints I.e. corresonding distances between ncs related molecules will be restrained. Covalent bonds and angles will not be included in these restraints. ---------------------------------------------------------------------------------------------- Scattering factors file : /net/anaconda/raid1/afonine/work/CCP4/ccp4-9/lib/data/atomsf.lib _ccp4_form_factor.scat_method 'Mott-Bethe' _ccp4_form_factor.scat_data_source electron Note that when Mott-Bethe formula is used then charges are ignored 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 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: 5094 0 5094 Angles: 9247 0 9247 Chirals: 398 0 398 Planes: 883 0 883 Torsions: 2194 0 2194 Intervals: 0 0 0 -------------------------------------------------------------------------------- Number of harmonic restraints = 0 Number of atoms in special position = 0 ----------------------------------------------------- **** Info from mtz file **** FreeR flag -999 Number of "free" reflections 0 Number of all reflections 62143 Warning ==>The number of free reflections with flag -999 is zero Warning ==> Switching off use of free R -------------------------------------------------------------------------------- Number of reflections in file 62143 Number of reflections read 62143 Current auto weighting coefficient = 1.96000004 ###### TLS Group Definitions ###### CGMAT cycle number = 1 Limits of asymmetric unit : 1.00 1.00 1.00 Grid spacing to be used : 180 96 140 Maximuum H,K,L : 42 23 33 Minimum acceptable grid spacing: 118 62 91 Weight matrix 2.62263184E-03 Actual weight 1.96000004 is applied to the X-ray term Norm of X_ray positional gradient 20.9 Norm of Geom. positional gradient 48.4 Norm of X_ray B-factor gradient 31.2 Norm of Geom. B-factor gradient 9.46 Product of X_ray and Geom posit. gradients -0.211E+07 Cosine of angle between them -0.138 Product of X_ray and Geom B-fact gradients -0.307E+05 Cosine of angle between them -0.021 Residuals: XRAY= 0.1038E+07 GEOM= 9641. TOTAL= 0.1048E+07 function value 1047581.38 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 2619 0.009 0.012 Bond distances: others 2475 0.000 0.016 Bond angles : refined atoms 3574 1.318 1.789 Bond angles : others 5673 0.409 1.751 Torsion angles, period 1. refined 327 5.114 5.000 Torsion angles, period 2. refined 25 0.284 5.000 Torsion angles, period 3. refined 396 15.875 10.000 Torsion angles, period 6. refined 113 15.355 10.000 Chiral centres: refined atoms 398 0.068 0.200 Planar groups: refined atoms 3199 0.004 0.020 Planar groups: others 633 0.002 0.020 VDW repulsions: refined_atoms 500 0.203 0.200 VDW repulsions.others 2318 0.249 0.200 VDW; torsion: refined_atoms 1334 0.184 0.200 VDW; torsion.others 1481 0.087 0.200 HBOND: refined_atoms 51 0.248 0.200 HBOND.others 4 0.127 0.200 M. chain bond B values: refined atoms 1323 1.851 6.100 M. chain bond B values: others 1322 1.852 6.100 M. chain angle B values: refined atoms 1645 2.876 10.929 M. chain angle B values: others 1646 2.875 10.928 S. chain bond B values: refined atoms 1296 0.913 6.071 S. chain bond B values: others 1296 0.913 6.071 S. chain angle B values: refined atoms 1929 1.378 11.138 S. chain angle B values: others 1930 1.378 11.137 Long range B values: refined atoms 2790 2.957 53.956 Long range B values: others 2790 2.957 53.954 ncsr local: group 1 977 0.259 0.050 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall scale should be multiplied by 1.0000 Overall : scale = 2.5189, B = 2.7418 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 1. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 1. M(Rfactor) v. resln :N:1,6,7: :Cycle 1. M(Fobs) and M(Fc) v. resln :N:1,4,5: :Cycle 1. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$ $$ 0.003 698 100.00 361.8 378.9 0.15 0.15 0.008 1279 100.00 151.9 148.3 0.23 0.23 0.014 1681 100.00 98.3 99.2 0.31 0.31 0.019 1933 100.00 79.1 81.8 0.34 0.34 0.025 2196 100.00 75.2 73.7 0.36 0.36 0.031 2452 100.00 83.3 74.9 0.34 0.34 0.036 2619 100.00 91.1 74.7 0.36 0.36 0.042 2901 100.00 94.2 69.1 0.40 0.40 0.047 3048 100.00 90.5 62.5 0.43 0.43 0.053 3229 100.00 80.3 52.7 0.46 0.46 0.058 3306 100.00 65.0 43.5 0.47 0.47 0.064 3585 100.00 49.9 36.2 0.47 0.47 0.069 3653 100.00 36.7 30.1 0.50 0.50 0.075 3828 100.00 29.9 26.4 0.53 0.53 0.081 3934 100.00 25.2 23.3 0.53 0.53 0.086 4146 100.00 20.1 20.5 0.59 0.59 0.092 4227 100.00 16.3 18.1 0.63 0.63 0.097 4330 100.00 14.0 16.4 0.66 0.66 0.103 4479 100.00 12.2 15.0 0.70 0.70 0.108 4619 100.00 10.9 13.7 0.71 0.71 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 1. FSC and Fom(