############################################################### ############################################################### ############################################################### ### CCP4 7.0.024: Refmac version 5.8.0158 : 03/10/16## ############################################################### User: unknown Run date: 2/12/2016 Run time: 15:22:21 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: $$ Main reference $$ "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 $$ $SUMMARY :Reference1: $$ 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 $$ $SUMMARY :Reference2: $$ Refmac: $$ :TEXT:Reference2: $$ Data line--- make check NONE Data line--- make hydrogen ALL hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO Data line--- refi type REST resi MLKF meth CGMAT bref ISOT Data line--- ncyc 10 Data line--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES Data line--- weight AUTO Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0 ncsr 10.0 Data line--- labin FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM Data line--- PNAME XDSproject Data line--- DNAME XDSdataset Data line--- RSIZE 80 Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /home/marek/Desktop/LYSOZYM-seminar/ccp4/lyso-2016-HD_sg96_refmac1.mtz !------------------------------------------------! ! ! ! Input mtz file seems to be output from refmac ! ! You should always use original mtz ! ! ! !------------------------------------------------! **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - /home/marek/Desktop/LYSOZYM-seminar/ccp4/3_arp_warp_classic/arp_5.pdb Output coordinate file. Logical name - XYZOUT actual file name - /home/marek/Desktop/LYSOZYM-seminar/ccp4/arp_5_refmac1.pdb Input reflection file. Logical name - HKLIN actual file name - /home/marek/Desktop/LYSOZYM-seminar/ccp4/lyso-2016-HD_sg96_refmac1.mtz Output reflection file. Logical name - HKLOUT actual file name - /home/marek/Desktop/LYSOZYM-seminar/ccp4/lyso-2016-HD_sg96_refmac2.mtz Cell from mtz : 78.715 78.715 37.084 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 : /home/marek/Downloads/destination/ccp4-7.0/lib/data/monomers/mon*cif Parameters for new entry and VDW: /home/marek/Downloads/destination/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 All links to sugar 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: 20 0.0208 Refinement of individual isotropic Bfactors Refinement resln : 55.6599 1.5500 Estimated number of reflections : 21848 Free R exclusion - flag equals: 0 Auto weighting. An attempt Refinement cycles : 10 Scaling type : Wilson using 1 Gaussian 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: 55.6599 1.5500 Damping factors: 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 --------------------------------------------------------------- Input file :/home/marek/Desktop/LYSOZYM-seminar/ccp4/3_arp_warp_classic/arp_5. ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 5.44 _lib_update 30/05/14 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 13482 with complete description : 13482 NUMBER OF MODIFICATIONS : 63 NUMBER OF LINKS : 73 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) FORMATTED OLD file opened on unit 45 Logical name: ATOMSF, Filename: /home/marek/Downloads/destination/ccp4-7.0/lib/data/atomsf.lib Number of atoms : 1146 Number of residues : 430 Number of chains : 3 I am reading library. Please wait. mon_lib.cif WARNING : link:SS is found dist = 2.063 ideal_dist= 2.031 ch:AA res: 30 CYS at:SG .->AA res: 115 CYS at:SG . WARNING : link:SS is found dist = 2.082 ideal_dist= 2.031 ch:AA res: 64 CYS at:SG .->AA res: 80 CYS at:SG . WARNING : link:SS is found dist = 2.050 ideal_dist= 2.031 ch:AA res: 76 CYS at:SG .->AA res: 94 CYS at:SG . INFO: link is found (not be used) dist= 1.647 ideal_dist= 1.420 ch:AA res: 102 ALA at:O .->ch:AA res: 104 GLY at:CA . -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:CD1 ILE 2 AA is missing in the structure ATTENTION: atom:CB LYS 4 AA is missing in the structure ATTENTION: atom:CG LYS 4 AA is missing in the structure ATTENTION: atom:CD LYS 4 AA is missing in the structure ATTENTION: atom:CE LYS 4 AA is missing in the structure ATTENTION: atom:NZ LYS 4 AA is missing in the structure ATTENTION: atom:CE LYS 5 AA is missing in the structure ATTENTION: atom:CG GLN 6 AA is missing in the structure ATTENTION: atom:CD GLN 6 AA is missing in the structure ATTENTION: atom:OE1 GLN 6 AA is missing in the structure ATTENTION: atom:SG CYS 9 AA is missing in the structure ATTENTION: atom:CG LYS 10 AA is missing in the structure ATTENTION: atom:CD LYS 10 AA is missing in the structure ATTENTION: atom:NZ LYS 10 AA is missing in the structure ATTENTION: atom:CG ASN 11 AA is missing in the structure ATTENTION: atom:OD1 ASN 11 AA is missing in the structure ATTENTION: atom:ND2 ASN 11 AA is missing in the structure ATTENTION: atom:CG LEU 12 AA is missing in the structure ATTENTION: atom:CD2 LEU 12 AA is missing in the structure ATTENTION: atom:CG2 VAL 13 AA is missing in the structure ... and more ... Number of chains : 3 Total number of monomers : 430 Number of atoms : 2246 Number of missing atoms : 101 Number of rebuilt atoms : 729 Number of unknown atoms : 0 Number of deleted atoms : 0 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 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 H 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7997 0.0030 O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 1.1842 CA 8.6266 10.4421 7.3873 0.6599 1.5899 85.7484 1.0211 178.4370 1.7125 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: 1469 0 1469 Angles: 2557 0 2557 Chirals: 118 0 118 Planes: 251 0 251 Torsions: 571 0 571 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 883 Number of all reflections 17455 -------------------------------------------------------------------------------- Number of reflections in file 17455 Number of reflections read 17455 ###### TLS Group Definitions ###### CGMAT cycle number = 1 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 62 TYR CD2 deviation= 0.22 sigma.= 0.02 Atom: A 62 TYR HD2 deviation= -0.25 sigma.= 0.02 Atom: A 65 HIS CD2 deviation= -0.28 sigma.= 0.02 Atom: A 65 HIS HD2 deviation= 0.26 sigma.= 0.02 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 1 LYS HE3 . - Z 248 DUM DUM . mod.= 0.711 id.= 1.100 dev= -0.39 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 1 LYS HE3 . - Z 248 DUM DUM . mod.= 0.711 id.= 1.100 dev= -0.39 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 3 LEU HD12. - Z 67 DUM DUM . mod.= 0.580 id.= 1.100 dev= -0.52 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 3 LEU HD12. - Z 67 DUM DUM . mod.= 0.580 id.= 1.100 dev= -0.52 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 3 LEU HD22. - Z 102 DUM DUM . mod.= 0.531 id.= 1.100 dev= -0.57 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 3 LEU HD22. - Z 102 DUM DUM . mod.= 0.531 id.= 1.100 dev= -0.57 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 6 GLN HB2 . - Z 20 DUM DUM . mod.= 0.738 id.= 1.100 dev= -0.36 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 6 GLN HB2 . - Z 20 DUM DUM . mod.= 0.738 id.= 1.100 dev= -0.36 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 7 GLU HB2 . - Z 216 DUM DUM . mod.= 0.679 id.= 1.100 dev= -0.42 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 7 GLU HB2 . - Z 216 DUM DUM . mod.= 0.679 id.= 1.100 dev= -0.42 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 12 LEU HB2 . - Z 80 DUM DUM . mod.= 0.732 id.= 1.100 dev= -0.37 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 12 LEU HB2 . - Z 80 DUM DUM . mod.= 0.732 id.= 1.100 dev= -0.37 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 13 VAL HG12. - Z 136 DUM DUM . mod.= 0.766 id.= 1.100 dev= -0.33 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 13 VAL HG12. - Z 136 DUM DUM . mod.= 0.766 id.= 1.100 dev= -0.33 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 15 GLN HG2 . - Z 62 DUM DUM . mod.= 0.898 id.= 1.100 dev= -0.20 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 15 GLN HG2 . - Z 62 DUM DUM . mod.= 0.898 id.= 1.100 dev= -0.20 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 17 MET HG2 . - Z 112 DUM DUM . mod.= 0.793 id.= 1.100 dev= -0.31 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 17 MET HG2 . - Z 112 DUM DUM . mod.= 0.793 id.= 1.100 dev= -0.31 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 19 GLY HA3 . - Z 120 DUM DUM . mod.= 0.530 id.= 1.100 dev= -0.57 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 19 GLY HA3 . - Z 120 DUM DUM . mod.= 0.530 id.= 1.100 dev= -0.57 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 23 ILE HD12. - Z 91 DUM DUM . mod.= 0.549 id.= 1.100 dev= -0.55 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 23 ILE HD12. - Z 91 DUM DUM . mod.= 0.549 id.= 1.100 dev= -0.55 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 26 PRO CG . - Z 164 DUM DUM . mod.= 0.932 id.= 1.820 dev= -0.89 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 26 PRO CG . - Z 164 DUM DUM . mod.= 0.932 id.= 1.820 dev= -0.89 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 33 PHE HE1 . - Z 239 DUM DUM . mod.= 0.295 id.= 1.100 dev= -0.80 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 33 PHE HE1 . - Z 239 DUM DUM . mod.= 0.295 id.= 1.100 dev= -0.80 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 41 ARG HD2 . - Z 27 DUM DUM . mod.= 0.589 id.= 1.100 dev= -0.51 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 41 ARG HD2 . - Z 27 DUM DUM . mod.= 0.589 id.= 1.100 dev= -0.51 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 68 LYS HZ1 . - Z 179 DUM DUM . mod.= 0.983 id.= 1.100 dev= -0.12 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 68 LYS HZ1 . - Z 179 DUM DUM . mod.= 0.983 id.= 1.100 dev= -0.12 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 68 LYS HZ2 . - Z 31 DUM DUM . mod.= 0.591 id.= 1.100 dev= -0.51 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 68 LYS HZ2 . - Z 31 DUM DUM . mod.= 0.591 id.= 1.100 dev= -0.51 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 74 ASN H . - Z 235 DUM DUM . mod.= 0.554 id.= 1.100 dev= -0.55 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 74 ASN H . - Z 235 DUM DUM . mod.= 0.554 id.= 1.100 dev= -0.55 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 75 ALA HB1 . - Z 37 DUM DUM . mod.= 0.687 id.= 1.100 dev= -0.41 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 75 ALA HB1 . - Z 37 DUM DUM . mod.= 0.687 id.= 1.100 dev= -0.41 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 77 ASN HB2 . - Z 106 DUM DUM . mod.= 0.747 id.= 1.100 dev= -0.35 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 77 ASN HB2 . - Z 106 DUM DUM . mod.= 0.747 id.= 1.100 dev= -0.35 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 79 SER HB2 . - Z 154 DUM DUM . mod.= 0.812 id.= 1.100 dev= -0.29 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 79 SER HB2 . - Z 154 DUM DUM . mod.= 0.812 id.= 1.100 dev= -0.29 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 79 SER H . - Z 68 DUM DUM . mod.= 0.533 id.= 1.100 dev= -0.57 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 79 SER H . - Z 68 DUM DUM . mod.= 0.533 id.= 1.100 dev= -0.57 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 85 ASP HA . - Z 77 DUM DUM . mod.= 0.881 id.= 1.100 dev= -0.22 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 85 ASP HA . - Z 77 DUM DUM . mod.= 0.881 id.= 1.100 dev= -0.22 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 90 ASP HA . - Z 125 DUM DUM . mod.= 0.658 id.= 1.100 dev= -0.44 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 90 ASP HA . - Z 125 DUM DUM . mod.= 0.658 id.= 1.100 dev= -0.44 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 92 LEU HB3 . - Z 76 DUM DUM . mod.= 0.660 id.= 1.100 dev= -0.44 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 92 LEU HB3 . - Z 76 DUM DUM . mod.= 0.660 id.= 1.100 dev= -0.44 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 99 ALA HB2 . - Z 158 DUM DUM . mod.= 0.631 id.= 1.100 dev= -0.47 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 99 ALA HB2 . - Z 158 DUM DUM . mod.= 0.631 id.= 1.100 dev= -0.47 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 99 ALA HB3 . - Z 30 DUM DUM . mod.= 0.671 id.= 1.100 dev= -0.43 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 99 ALA HB3 . - Z 30 DUM DUM . mod.= 0.671 id.= 1.100 dev= -0.43 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 100 GLY HA3 . - Z 66 DUM DUM . mod.= 0.524 id.= 1.100 dev= -0.58 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 100 GLY HA3 . - Z 66 DUM DUM . mod.= 0.524 id.= 1.100 dev= -0.58 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 101 GLU H . - Z 184 DUM DUM . mod.= 0.613 id.= 1.100 dev= -0.49 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 101 GLU H . - Z 184 DUM DUM . mod.= 0.613 id.= 1.100 dev= -0.49 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 106 THR HG21. - Z 177 DUM DUM . mod.= 0.392 id.= 1.100 dev= -0.71 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 106 THR HG21. - Z 177 DUM DUM . mod.= 0.392 id.= 1.100 dev= -0.71 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 112 LYS HB3 . - Z 205 DUM DUM . mod.= 0.916 id.= 1.100 dev= -0.18 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 112 LYS HB3 . - Z 205 DUM DUM . mod.= 0.916 id.= 1.100 dev= -0.18 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 113 SER HB2 . - Z 265 DUM DUM . mod.= 0.220 id.= 1.100 dev= -0.88 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 113 SER HB2 . - Z 265 DUM DUM . mod.= 0.220 id.= 1.100 dev= -0.88 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 116 ARG HG2 . - Z 45 DUM DUM . mod.= 0.609 id.= 1.100 dev= -0.49 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 116 ARG HG2 . - Z 45 DUM DUM . mod.= 0.609 id.= 1.100 dev= -0.49 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 118 HIS HB2 . - Z 25 DUM DUM . mod.= 0.553 id.= 1.100 dev= -0.55 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 118 HIS HB2 . - Z 25 DUM DUM . mod.= 0.553 id.= 1.100 dev= -0.55 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 120 LEU HG . - Z 34 DUM DUM . mod.= 0.934 id.= 1.100 dev= -0.17 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 120 LEU HG . - Z 34 DUM DUM . mod.= 0.934 id.= 1.100 dev= -0.17 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 120 LEU HD21. - Z 142 DUM DUM . mod.= 0.619 id.= 1.100 dev= -0.48 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 120 LEU HD21. - Z 142 DUM DUM . mod.= 0.619 id.= 1.100 dev= -0.48 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 120 LEU HD22. - Z 53 DUM DUM . mod.= 0.561 id.= 1.100 dev= -0.54 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 120 LEU HD22. - Z 53 DUM DUM . mod.= 0.561 id.= 1.100 dev= -0.54 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 121 SER H . - Z 114 DUM DUM . mod.= 0.925 id.= 1.100 dev= -0.17 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 121 SER H . - Z 114 DUM DUM . mod.= 0.925 id.= 1.100 dev= -0.17 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 123 PHE HD1 . - Z 288 DUM DUM . mod.= 0.615 id.= 1.100 dev= -0.48 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 123 PHE HD1 . - Z 288 DUM DUM . mod.= 0.615 id.= 1.100 dev= -0.48 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 A 123 PHE HE1 . - Z 61 DUM DUM . mod.= 0.992 id.= 1.100 dev= -0.11 sig.= 0.30 sym.= 1 0 0 0 ncs -1 type = 5 A 123 PHE HE1 . - Z 61 DUM DUM . mod.= 0.992 id.= 1.100 dev= -0.11 sig.= 0.30 sym.= 1 0 0 0 ncs 1 type = 5 Limits of asymmetric unit : 1.00 1.00 0.13 Grid spacing to be used : 176 176 88 Maximuum H,K,L : 51 51 24 Minimum acceptable grid spacing: 116 116 55 Limits of asymmetric unit : 1.00 1.00 0.13 Grid spacing to be used : 176 176 88 Maximuum H,K,L : 51 51 24 Minimum acceptable grid spacing: 116 116 55 Weight matrix 0.84620386 Actual weight 10.000000 is applied to the X-ray term Norm of X_ray positional gradient 69.8 Norm of Geom. positional gradient 54.5 Norm of X_ray B-factor gradient 632. Norm of Geom. B-factor gradient 0.185E+05 Product of X_ray and Geom posit. gradients -0.465E+07 Cosine of angle between them -0.225 Product of X_ray and Geom B-fact gradients -0.254E+08 Cosine of angle between them -0.001 Residuals: XRAY= 0.8496E+06 GEOM= 0.4800E+05 TOTAL= 0.8976E+06 function value 897613.56 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 808 0.020 0.019 Bond distances: others 661 0.000 0.020 Bond angles : refined atoms 1075 1.961 1.909 Bond angles : others 1482 4.199 3.000 Torsion angles, period 1. refined 112 7.020 5.000 Torsion angles, period 2. refined 26 30.174 25.000 Torsion angles, period 3. refined 100 13.531 15.000 Chiral centres: refined atoms 118 0.154 0.200 Planar groups: refined atoms 932 0.017 0.020 Planar groups: others 166 0.032 0.020 VDW repulsions: refined_atoms 466 0.325 0.200 VDW repulsions.others 1228 0.264 0.200 VDW; torsion: refined_atoms 820 0.174 0.200 VDW; torsion.others 674 0.104 0.200 HBOND: refined_atoms 38 0.340 0.200 HBOND.others 2 0.181 0.200 DUMMY_NORMAL: refined_atoms 110 0.245 0.300 DUMMY_NORMAL.others 84 0.445 0.300 DUMMY_DUMMY: refined_atoms 22 0.088 0.300 VDW repulsions: symmetry: refined_atoms 8 0.354 0.200 VDW repulsions: symmetry: others 16 0.372 0.200 HBOND: symmetry: refined_atoms 1 0.290 0.200 DUMMY_NORMAL: symmetry: refined_atoms 1 0.013 0.300 DUMMY_NORMAL: symmetry: others 1 0.007 0.300 M. chain bond B values: refined atoms 461 1.261 1.170 M. chain bond B values: others 462 1.538 1.169 M. chain angle B values: refined atoms 566 1.684 1.738 M. chain angle B values: others 566 1.850 1.734 S. chain bond B values: refined atoms 347 2.027 1.252 S. chain bond B values: others 348 2.024 1.259 S. chain angle B values: refined atoms 509 2.408 1.781 S. chain angle B values: others 510 2.850 1.780 Long range B values: refined atoms 1030 3.904 14.642 Long range B values: others 1016 3.897 14.677 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 0.979, B = 0.354 Partial structure 1: scale = 0.377, B = 49.148 Overall anisotropic scale factors B11 = 0.00 B22 = 0.00 B33 = -0.00 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.