############################################################### ############################################################### ############################################################### ### CCP4 7.0.078: Refmac version 5.8.0258 : 09/10/19## ############################################################### User: maly Run date: 28/ 5/2020 Run time: 11:43:08 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--- 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--- scal type SIMP LSSC ANISO EXPE Data line--- solvent YES Data line--- weight MATRIX 0.048 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--- PNAME BO+Fe Data line--- DNAME BF19 Data line--- RSIZE 80 Data line--- refi reso 47.35 2.80 Data line--- ncyc 10 Data line--- bins 9 Data line--- weight matrix 0.0480 Data line--- monitor MEDIum Data line--- free 0 Data line--- END OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: BO_R.mtz LABIN FP=FP SIGFP=SIGFP FREE=FreeR_flag **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - BO_from2-80A_2-80A_modified.pdb Output coordinate file. Logical name - XYZOUT actual file name - BO_from2-80A_R00_2-80A.pdb Input reflection file. Logical name - HKLIN actual file name - BO_R.mtz Output reflection file. Logical name - HKLOUT actual file name - BO_from2-80A_R00_2-80A.mtz Cell from mtz : 134.507 204.057 226.976 90.000 90.000 90.000 Space group from mtz: number - 22; name - F 2 2 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 User supplied dictionary entries: merge_TRP-HIS_FC6.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: 9 0.0142 Refinement of individual isotropic Bfactors Refinement resln : 47.3545 2.8000 Estimated number of reflections : 51329 Free R exclusion - flag equals: 0 Weighting by comparison of trace of matrix Weighting parameters : 0.0480 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: 47.3545 2.8000 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 --------------------------------------------------------------- Input file :BO_from2-80A_2-80A_modified.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 5.51 _lib_update 11/07/18 ------------------------------ ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name ? _lib_version ? _lib_update ? ------------------------------ WARNING: duplicated name of monomer FC6 Last entry will be used. NUMBER OF MONOMERS IN THE LIBRARY : 24624 with complete description : 24624 NUMBER OF MODIFICATIONS : 72 NUMBER OF LINKS : 78 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) Number of atoms : 9511 Number of residues : 1660 Number of chains : 49 I am reading library. Please wait. mon_lib.cif WARNING : CIS peptide bond is found, angle = 5.25 ch:AAA res: 66 SER --> 67 PRO WARNING : CIS peptide bond is found, angle = 10.14 ch:AAA res: 447 ALA --> 448 PRO WARNING : CIS peptide bond is found, angle = 4.63 ch:AAA res: 465 HIS --> 466 ASP WARNING : CIS peptide bond is found, angle = 0.55 ch:BBB res: 66 SER --> 67 PRO WARNING : CIS peptide bond is found, angle = 7.13 ch:BBB res: 447 ALA --> 448 PRO WARNING : CIS peptide bond is found, angle = 0.00 ch:BBB res: 465 HIS --> 466 ASP INFO: link is found (not be used) dist= 2.604 ideal_dist= 2.275 ch:AAA res: 63 ASP at:OD2 .->ch:AuA res:1002 NA at:NA . INFO: link is found (not be used) dist= 2.965 ideal_dist= 2.305 ch:AAA res: 86 ASN at:O .->ch:AvA res:1003 NA at:NA . INFO: link is found (not be used) dist= 1.836 ideal_dist= 2.075 ch:AAA res: 94 HIS at:NE2 .->ch:AdA res: 604 CU at:CU . INFO: link is found (not be used) dist= 2.056 ideal_dist= 2.075 ch:AAA res: 96 HIS at:ND1 .->ch:AcA res: 603 CU at:CU . INFO: link is found (not be used) dist= 2.000 ideal_dist= 2.075 ch:AAA res: 134 HIS at:NE2 .->ch:AcA res: 603 CU at:CU . INFO: link is found (not be used) dist= 1.922 ideal_dist= 2.075 ch:AAA res: 136 HIS at:NE2 .->ch:AbA res: 602 CU at:CU . INFO: link is found (not be used) dist= 3.102 ideal_dist= 2.434 ch:AAA res: 284 SER at:OG .->ch:AwA res:1004 NA at:NA . INFO: link is found (not be used) dist= 2.523 ideal_dist= 2.305 ch:AAA res: 285 ASP at:OD1 .->ch:AwA res:1004 NA at:NA . INFO: link is found (not be used) dist= 1.396 ideal_dist= 1.410 ch:AAA res: 396 TRP at:CD1 .->ch:AAA res: 398 HIS at:NE2 . INFO: link is found (not be used) dist= 2.090 ideal_dist= 2.075 ch:AAA res: 398 HIS at:ND1 .->ch:AaA res: 601 CU at:CU . INFO: link is found (not be used) dist= 1.810 ideal_dist= 2.075 ch:AAA res: 401 HIS at:NE2 .->ch:AdA res: 604 CU at:CU . INFO: link is found (not be used) dist= 1.960 ideal_dist= 2.075 ch:AAA res: 403 HIS at:NE2 .->ch:AbA res: 602 CU at:CU . INFO: link is found (not be used) dist= 2.785 ideal_dist= 2.305 ch:AAA res: 404 LEU at:O .->ch:AxA res:1005 NA at:NA . INFO: link is found (not be used) dist= 2.683 ideal_dist= 2.305 ch:AAA res: 447 ALA at:O .->ch:AxA res:1005 NA at:NA . INFO: link is found (not be used) dist= 2.036 ideal_dist= 2.075 ch:AAA res: 456 HIS at:NE2 .->ch:AbA res: 602 CU at:CU . INFO: link is found (not be used) dist= 2.163 ideal_dist= 2.400 ch:AAA res: 457 CYS at:SG .->ch:AaA res: 601 CU at:CU . INFO: link is found (not be used) dist= 2.185 ideal_dist= 2.075 ch:AAA res: 458 HIS at:NE2 .->ch:AcA res: 603 CU at:CU . INFO: link is found (not be used) dist= 2.166 ideal_dist= 2.075 ch:AAA res: 462 HIS at:ND1 .->ch:AaA res: 601 CU at:CU . WARNING : link:NAG-ASN is found dist = 1.457 ideal_dist= 1.439 ch:AAA res: 472 ASN at:ND2 .->AeA res: 701 NAG at:C1 . WARNING : link:NAG-ASN is found dist = 1.448 ideal_dist= 1.439 ch:AAA res: 482 ASN at:ND2 .->AjA res: 711 NAG at:C1 . INFO: link is found (not be used) dist= 3.046 ideal_dist= 2.305 ch:AAA res: 525 GLU at:OE1 .->ch:AtA res:1001 NA at:NA . WARNING : link:BETA1-4 is found dist = 1.451 ideal_dist= 1.439 ch:AeA res: 701 NAG at:O4 .->AfA res: 702 NAG at:C1 . WARNING : link:BETA1-4 is found dist = 1.411 ideal_dist= 1.439 ch:AfA res: 702 NAG at:O4 .->AgA res: 703 BMA at:C1 . WARNING : link:ALPHA1-3 is found dist = 1.490 ideal_dist= 1.439 ch:AgA res: 703 BMA at:O3 .->AhA res: 704 MAN at:C1 . WARNING : link:ALPHA1-6 is found dist = 1.471 ideal_dist= 1.439 ch:AgA res: 703 BMA at:O6 .->AiA res: 705 MAN at:C1 . WARNING : link:BETA1-4 is found dist = 1.432 ideal_dist= 1.439 ch:AjA res: 711 NAG at:O4 .->AkA res: 712 NAG at:C1 . WARNING : link:NAG-NA is found dist = 2.355 ideal_dist= 2.434 ch:AjA res: 711 NAG at:O6 .->AtA res:1001 NA at:NA . WARNING : link:BETA1-4 is found dist = 1.451 ideal_dist= 1.439 ch:AkA res: 712 NAG at:O4 .->AlA res: 713 BMA at:C1 . INFO: link is found (not be used) dist= 1.832 ideal_dist= 2.075 ch:BBB res: 94 HIS at:NE2 .->ch:BdB res: 604 CU at:CU . INFO: link is found (not be used) dist= 2.174 ideal_dist= 2.075 ch:BBB res: 96 HIS at:ND1 .->ch:BcB res: 603 CU at:CU . INFO: link is found (not be used) dist= 2.119 ideal_dist= 2.075 ch:BBB res: 134 HIS at:NE2 .->ch:BcB res: 603 CU at:CU . INFO: link is found (not be used) dist= 1.917 ideal_dist= 2.075 ch:BBB res: 136 HIS at:NE2 .->ch:BbB res: 602 CU at:CU . INFO: link is found (not be used) dist= 2.508 ideal_dist= 2.275 ch:BBB res: 261 GLU at:OE2 .->ch:BtB res:1003 NA at:NA . INFO: link is found (not be used) dist= 2.580 ideal_dist= 2.305 ch:BBB res: 285 ASP at:OD1 .->ch:BsB res:1002 NA at:NA . INFO: link is found (not be used) dist= 2.672 ideal_dist= 2.305 ch:BBB res: 338 ASP at:OD1 .->ch:BtB res:1003 NA at:NA . INFO: link is found (not be used) dist= 1.388 ideal_dist= 1.410 ch:BBB res: 396 TRP at:CD1 .->ch:BBB res: 398 HIS at:NE2 . INFO: link is found (not be used) dist= 2.021 ideal_dist= 2.075 ch:BBB res: 398 HIS at:ND1 .->ch:BaB res: 601 CU at:CU . INFO: link is found (not be used) dist= 1.923 ideal_dist= 2.075 ch:BBB res: 401 HIS at:NE2 .->ch:BdB res: 604 CU at:CU . INFO: link is found (not be used) dist= 2.078 ideal_dist= 2.075 ch:BBB res: 403 HIS at:NE2 .->ch:BbB res: 602 CU at:CU . INFO: link is found (not be used) dist= 1.954 ideal_dist= 2.075 ch:BBB res: 456 HIS at:NE2 .->ch:BbB res: 602 CU at:CU . INFO: link is found (not be used) dist= 2.137 ideal_dist= 2.400 ch:BBB res: 457 CYS at:SG .->ch:BaB res: 601 CU at:CU . INFO: link is found (not be used) dist= 2.311 ideal_dist= 2.075 ch:BBB res: 458 HIS at:NE2 .->ch:BcB res: 603 CU at:CU . INFO: link is found (not be used) dist= 2.095 ideal_dist= 2.075 ch:BBB res: 462 HIS at:ND1 .->ch:BaB res: 601 CU at:CU . WARNING : link:NAG-ASN is found dist = 1.440 ideal_dist= 1.439 ch:BBB res: 472 ASN at:ND2 .->BeB res: 701 NAG at:C1 . WARNING : link:NAG-ASN is found dist = 1.418 ideal_dist= 1.439 ch:BBB res: 482 ASN at:ND2 .->BiB res: 711 NAG at:C1 . INFO: link is found (not be used) dist= 3.021 ideal_dist= 2.305 ch:BBB res: 522 THR at:O .->ch:BrB res:1001 NA at:NA . INFO: link is found (not be used) dist= 2.986 ideal_dist= 2.305 ch:BBB res: 525 GLU at:OE1 .->ch:BrB res:1001 NA at:NA . WARNING : link:BETA1-4 is found dist = 1.449 ideal_dist= 1.439 ch:BeB res: 701 NAG at:O4 .->BfB res: 702 NAG at:C1 . WARNING : link:BETA1-4 is found dist = 1.415 ideal_dist= 1.439 ch:BfB res: 702 NAG at:O4 .->BgB res: 703 BMA at:C1 . WARNING : link:ALPHA1-3 is found dist = 1.471 ideal_dist= 1.439 ch:BgB res: 703 BMA at:O3 .->BhB res: 704 MAN at:C1 . WARNING : link:BETA1-4 is found dist = 1.455 ideal_dist= 1.439 ch:BiB res: 711 NAG at:O4 .->BjB res: 712 NAG at:C1 . WARNING : link:NAG-NA is found dist = 2.326 ideal_dist= 2.434 ch:BiB res: 711 NAG at:O6 .->BrB res:1001 NA at:NA . -------------------------------- --- title of input coord file --- PDB_code:xxxx PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- ATTENTION: atom:OXT ASP 533 BBB is missing in the structure Number of chains : 49 Total number of monomers : 1660 Number of atoms : 19000 Number of missing atoms : 0 Number of rebuilt atoms : 8394 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 CU 13.3445 3.5828 7.1711 0.2470 5.6185 11.3966 1.6743 64.8126 1.2284 FE 11.7738 4.7611 7.3600 0.3072 3.5235 15.3535 2.3054 76.8805 1.3103 NA 4.7659 3.2850 3.1758 8.8422 1.2683 0.3136 1.1136 129.4240 0.7258 CL 11.4601 0.0104 7.1962 1.1662 6.2554 18.5194 1.6455 47.7784 -9.3638 -------------------------------------------------------------------------------- External restraints group : 1 External restraints file :input_keywords Fail if one of the atoms involved in the restraints is missing in the pdb file Use restraints for all defined atoms Ignore restraints if abs(dmod-drest) > 50.000000 *sigma Ignore retraints if input dist > 1.00000003E+32 Weight scale sigmas : scale bond(dist) sigma : 1.0000000 scale angle sigma : 1.0000000 scale torsion sigma : 1.0000000 scale plane sigma : 1.0000000 scale chiral sigma : 1.0000000 scale interval sigma : 1.0000000 Weight min sigma : 0.0000000 Weight max sigma : 100.00000 GM parameter : 1.99999996E-02 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: 17141 0 17141 Angles: 31081 0 31081 Chirals: 1196 0 1196 Planes: 2666 0 2666 Torsions: 9145 0 9145 Intervals: 0 0 0 -------------------------------------------------------------------------------- **** Harmonic special positions restraints **** Harmonic restraints: sum 1/sigma^2 (x-x_c)^2 x - position of atoms, x_c - current positions Special positions sum 1/sigma^2(x-sum (R_sym x +t_sym))^2 x - position of atom, (R_sym,t_sym) are set of symmetry operators for which x =R_sym x +t_sym) Data line--- external harmonic residues from 801 A to 804 A sigma 0.03 Data line--- external harmonic residues from 801 B to 805 B sigma 0.03 Data line--- external harmonic residues from 139 B to 139 B sigma 0.01 Data line--- external harmonic residues from 274 B to 274 B sigma 0.01 Number of harmonic restraints = 191 Number of atoms in special position = 0 ----------------------------------------------------- **** Info from mtz file **** FreeR flag 0 Number of "free" reflections 1940 Number of all reflections 38477 -------------------------------------------------------------------------------- Number of reflections in file 72569 Number of reflections read 38477 Current auto weighting coefficient = 9.4992666 mode : HKRF ###### TLS Group Definitions ###### CGMAT cycle number = 1 **** Bond distance outliers **** Bond distance deviations from the ideal >10.000Sigma will be monitored B 401 HIS N . - B 401 HIS CA . mod.= 1.384 id.= 1.488 dev= 0.104 sig.= 0.010 **** Bond angle outliers **** Bond angle deviations from the ideal >10.000Sigma will be monitored A 701 NAG H1 - A 701 NAG C2 mod.= 144.04 id.= 108.34 dev=-35.698 sig.= 3.000 A 701 NAG O4 - A 702 NAG H1 mod.= 58.78 id.= 109.47 dev= 50.687 sig.= 3.000 A 702 NAG H1 - A 702 NAG C2 mod.= 140.26 id.= 108.34 dev=-31.916 sig.= 3.000 A 702 NAG O4 - A 703 BMA H1 mod.= 54.98 id.= 109.47 dev= 54.494 sig.= 3.000 A 703 BMA H1 - A 703 BMA C2 mod.= 145.24 id.= 108.34 dev=-36.905 sig.= 3.000 A 703 BMA O6 - A 705 MAN H1 mod.= 49.17 id.= 109.47 dev= 60.302 sig.= 3.000 A 703 BMA O3 - A 704 MAN H1 mod.= 52.00 id.= 109.47 dev= 57.469 sig.= 3.000 A 704 MAN H1 - A 704 MAN C2 mod.= 138.91 id.= 108.34 dev=-30.572 sig.= 3.000 A 705 MAN H1 - A 705 MAN C2 mod.= 139.42 id.= 108.34 dev=-31.083 sig.= 3.000 A 711 NAG H1 - A 711 NAG C2 mod.= 142.40 id.= 108.34 dev=-34.063 sig.= 3.000 A 711 NAG O4 - A 712 NAG H1 mod.= 54.50 id.= 109.47 dev= 54.965 sig.= 3.000 A 712 NAG H1 - A 712 NAG C2 mod.= 138.68 id.= 108.34 dev=-30.335 sig.= 3.000 A 712 NAG O4 - A 713 BMA H1 mod.= 53.58 id.= 109.47 dev= 55.894 sig.= 3.000 A 713 BMA H1 - A 713 BMA C2 mod.= 141.03 id.= 108.34 dev=-32.689 sig.= 3.000 B 701 NAG H1 - B 701 NAG C2 mod.= 141.38 id.= 108.34 dev=-33.037 sig.= 3.000 B 701 NAG O4 - B 702 NAG H1 mod.= 57.82 id.= 109.47 dev= 51.655 sig.= 3.000 B 702 NAG H1 - B 702 NAG C2 mod.= 142.67 id.= 108.34 dev=-34.329 sig.= 3.000 B 702 NAG O4 - B 703 BMA H1 mod.= 50.39 id.= 109.47 dev= 59.083 sig.= 3.000 B 703 BMA H1 - B 703 BMA C2 mod.= 141.59 id.= 108.34 dev=-33.255 sig.= 3.000 B 703 BMA O3 - B 704 MAN H1 mod.= 52.23 id.= 109.47 dev= 57.244 sig.= 3.000 B 704 MAN H1 - B 704 MAN C2 mod.= 138.51 id.= 108.34 dev=-30.169 sig.= 3.000 B 711 NAG O4 - B 712 NAG H1 mod.= 53.35 id.= 109.47 dev= 56.115 sig.= 3.000 B 712 NAG H1 - B 712 NAG C2 mod.= 139.09 id.= 108.34 dev=-30.750 sig.= 3.000 **** Large deviation of atoms from planarity **** Deviations from the planarity >10.000Sigma will be monitored Atom: A 24 ARG CD deviation= -0.27 sigma.= 0.02 Atom: A 24 ARG HE deviation= 0.27 sigma.= 0.02 Atom: A 125 ARG CD deviation= 0.33 sigma.= 0.02 Atom: A 125 ARG HE deviation= -0.32 sigma.= 0.02 Atom: A 317 ARG CD deviation= 0.24 sigma.= 0.02 Atom: A 317 ARG HE deviation= -0.24 sigma.= 0.02 Atom: A 497 ARG CD deviation= -0.34 sigma.= 0.02 Atom: A 497 ARG HE deviation= 0.34 sigma.= 0.02 Atom: B 125 ARG CD A deviation= -0.21 sigma.= 0.02 Atom: B 125 ARG HE A deviation= 0.21 sigma.= 0.02 Atom: B 125 ARG CD B deviation= -0.38 sigma.= 0.02 Atom: B 125 ARG HE B deviation= 0.37 sigma.= 0.02 Atom: B 294 ARG CD deviation= 0.65 sigma.= 0.02 Atom: B 294 ARG HE deviation= -0.64 sigma.= 0.02 Atom: B 356 ARG CD A deviation= -0.25 sigma.= 0.02 Atom: B 356 ARG HE A deviation= 0.25 sigma.= 0.02 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored A 396 TRP HD1 . - A 398 HIS NE2 . mod.= 0.499 id.= 2.750 dev= -2.25 sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 B 396 TRP HD1 . - B 398 HIS NE2 . mod.= 0.536 id.= 2.750 dev= -2.21 sig.= 0.20 sym.= 1 0 0 0 ncs 1 type = 1 Limits of asymmetric unit : 1.00 1.00 0.25 Grid spacing to be used : 196 300 336 Maximuum H,K,L : 49 74 82 Minimum acceptable grid spacing: 131 199 221 Limits of asymmetric unit : 1.00 1.00 0.25 Grid spacing to be used : 196 300 336 Maximuum H,K,L : 49 74 82 Minimum acceptable grid spacing: 131 199 221 Weight matrix 4.80000041E-02 Actual weight 16.397293 is applied to the X-ray term Norm of X_ray positional gradient 35.3 Norm of Geom. positional gradient 148. Norm of X_ray B-factor gradient 114. Norm of Geom. B-factor gradient 0.00 Product of X_ray and Geom posit. gradients -0.142E+08 Cosine of angle between them -0.052 Product of X_ray and Geom B-fact gradients 0.00 Cosine of angle between them 0.000 Residuals: XRAY= 0.4486E+07 GEOM= 0.7187E+05 TOTAL= 0.4558E+07 function value 4558193.0 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 9225 0.021 0.013 Bond distances: others 7916 0.035 0.017 Bond angles : refined atoms 12685 1.889 1.702 Bond angles : others 18396 2.833 1.594 Torsion angles, period 1. refined 1092 7.574 5.000 Torsion angles, period 2. refined 517 32.094 21.915 Torsion angles, period 3. refined 1292 14.814 15.000 Torsion angles, period 4. refined 63 19.358 15.000 Chiral centres: refined atoms 1196 0.101 0.200 Planar groups: refined atoms 10355 0.015 0.020 Planar groups: others 2034 0.032 0.020 VDW repulsions: refined_atoms 1745 0.219 0.200 VDW repulsions.others 7770 0.225 0.200 VDW; torsion: refined_atoms 4212 0.176 0.200 VDW; torsion.others 3848 0.105 0.200 HBOND: refined_atoms 503 0.144 0.200 HBOND.others 6 0.086 0.200 Metal-ion: refined_atoms 11 0.126 0.200 VDW repulsions: symmetry: refined_atoms 16 0.205 0.200 VDW repulsions: symmetry: others 42 0.191 0.200 HBOND: symmetry: refined_atoms 7 0.141 0.200 M. chain bond B values: refined atoms 4328 0.000 3.653 M. chain bond B values: others 4327 0.000 3.653 M. chain angle B values: refined atoms 5426 0.000 5.480 M. chain angle B values: others 5427 0.000 5.480 S. chain bond B values: refined atoms 4896 0.000 3.653 S. chain bond B values: others 4897 0.000 3.653 S. chain angle B values: refined atoms 7255 0.000 5.480 S. chain angle B values: others 7256 0.000 5.480 Long range B values: refined atoms 9962 0.000 41.983 Long range B values: others 9872 0.000 41.854 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall scale should be multiplied by 1.0000 Overall : scale = 0.0051, B = 4.8855 Partial structure 1: scale = 0.3843, B = 14.9662 Overall anisotropic scale factors B11 = -1.35 B22 = -1.58 B33 = 2.93 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.