#CCP4I VERSION CCP4Interface 1.3.13 #CCP4I SCRIPT LOG refmac5 #CCP4I DATE 19 Sep 2003 14:58:24 #CCP4I USER mgwt #CCP4I PROJECT 2003test #CCP4I JOB_ID 182 #CCP4I SCRATCH /tmp/mgwt #CCP4I HOSTNAME bunyip #CCP4I PID 2564 ############################################################### ############################################################### ############################################################### ### CCP4 5.0: Refmac_5.1.9999 5.1.9999 ########## ############################################################### User: mgwt Run date: 19/ 9/2003 Run time: 14:58:24 Please reference: Collaborative Computational Project, Number 4. 1994. "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. $TEXT:Reference1: $$ comment $$ "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 $$ $SUMMARY :Reference1: $$ Refmac: $$ :TEXT:Reference1: $$ Data line--- make check NONE Data line--- make hydrogen ALL hout NO peptide NO cispeptide YES ssbridge YES chain NO symmetry YES sugar YES connectivity NO link NO Data line--- nonx nchains 3 chnid A B C nspa 0 Data line--- refi type REST resi MLKF meth CGMAT bref ISOT Data line--- ncyc 5 Data line--- bins 20 Data line--- scal type BULK LSSC ANISO ncycles 10 Data line--- weight MATRIX 0.5 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 SIGFP=SIGF FREE=FreeR_flag Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM Data line--- NOHARVEST Comment line--- # External script file: Data line--- END Dataset id missing from COLUMN records in MTZ header. Making default assignments. >>>>>> CCP4 library signal mtz:Missing or incomplete dataset information in input file. (Warning) raised in MtzGet <<<<<< OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /y/people/mgwt/CCP4/examples/tut2003/data/cardiotoxin.mtz **** Input and Default parameters# **** Input coordinate file. Logical name - XYZIN actual file name - /y/people/mgwt/TEST/model_molrep2.pdb Output coordinate file. Logical name - XYZOUT actual file name - /y/people/mgwt/work/2003test_182_2_pdb_1.tmp Input reflection file. Logical name - HKLIN actual file name - /y/people/mgwt/CCP4/examples/tut2003/data/cardiotoxin.mtz Output reflection file. Logical name - HKLOUT actual file name - /y/people/mgwt/work/2003test_182_4_mtz_1.tmp Cell from mtz : 78.700 40.400 56.000 90.000 117.100 90.000 Space group from mtz: number - 5; name - C2 Refinement type : Restrained **** Makecif parameters **** Dictionary files for restraints : /y/programs/xtal/ccp4-5.0.d/lib/data/monomers/mon*cif Parameters for new entry and VDW: /y/programs/xtal/ccp4-5.0.d/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 Bulk solvent based on Babinet"s principle 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 Method of minimisation : Sparse Matrix Experimental sigmas used for weighting Number of Bins and width: 20 0.0211 Refinement of individual isotropic Bfactors Refinement resln : 50.0000 1.5386 Estimated number of reflections : 33246 Free R exclusion - flag equals: 0 Weighting by comparison of trace of matrix Weighting parameters : 0.5000 Refinement cycles : 5 Scaling type : Bulk solvent using using Babinet principle using working set of reflns but not experimental sigmas Estimation of SigmaA Using 2 Gaussians: using free set of reflns with experimental sigmas using free set of reflns with experimental sigmas Scaling and SigmaA resln: 50.0000 1.5386 Damping factors: 1.0000 1.0000 **** Geometry restraints and weights **** Sigma: Bonding distances Weight = 1.00 Bond angles Weight = 1.00 Planar groups WEIGHT= 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) 1.50A**2 Main chain angle (1-3 neighbour) 2.00A**2 Side chain bond 3.00A**2 Side chain angle 4.50A**2 **** NCS restraints parameters **** Number of different NCS restraints 1 NCS restraint : 1 Number of chains : 3 Chain names : A B C Spans 1 Span 1, From -9999 to 99999, weighting code 0 Weight= 1.00 Positional, tight class 0.05A Positional, medium class 0.50A Positional, weak class 5.00A Thermal, tight class 0.50A**2 Thermal, medium class 2.00A**2 Thermal, weak class 10.00A**2 RESTRAINTS AGAINST EXCESSIVE SHIFTS Positional parameters 0.00A Thermal parameters 0.00A Occupancy parameters 0.00 RADIUS OF CONFIDENCE Positional parameters 0.30A Thermal parameters 0.03A**2 Occupancy parameters 0.50 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 NCS outliers 10.000 --------------------------------------------------------------- Input file :/y/people/mgwt/TEST/model_molrep2.pdb ------------------------------ --- LIBRARY OF MONOMERS --- _lib_name mon_lib _lib_version 4.3 _lib_update 11/06/03 ------------------------------ NUMBER OF MONOMERS IN THE LIBRARY : 2432 with complete description : 449 NUMBER OF MODIFICATIONS : 43 NUMBER OF LINKS : 64 I am reading libraries. Please wait. - energy parameters - monomer"s description (links & mod ) FORMATTED OLD file opened on unit 45 Logical name: ATOMSF, Full name: /y/programs/xtal/ccp4-5.0.d/lib/data/atomsf.lib Number of atoms : 936 Number of residues : 150 Number of chains : 3 I am reading library. Please wait. mon_lib.cif WARNING : link:SS is found dist = 2.043 ideal_dist= 2.031 ch:AA res: 3 CYS at:SG .->AA res: 21 CYS at:SG . WARNING : link:SS is found dist = 2.062 ideal_dist= 2.031 ch:AA res: 14 CYS at:SG .->AA res: 38 CYS at:SG . WARNING : link:SS is found dist = 2.052 ideal_dist= 2.031 ch:AA res: 42 CYS at:SG .->AA res: 53 CYS at:SG . WARNING : link:SS is found dist = 2.030 ideal_dist= 2.031 ch:AA res: 54 CYS at:SG .->AA res: 59 CYS at:SG . WARNING : link:SS is found dist = 2.042 ideal_dist= 2.031 ch:BB res: 3 CYS at:SG .->BB res: 21 CYS at:SG . WARNING : link:SS is found dist = 2.061 ideal_dist= 2.031 ch:BB res: 14 CYS at:SG .->BB res: 38 CYS at:SG . WARNING : link:SS is found dist = 2.053 ideal_dist= 2.031 ch:BB res: 42 CYS at:SG .->BB res: 53 CYS at:SG . WARNING : link:SS is found dist = 2.030 ideal_dist= 2.031 ch:BB res: 54 CYS at:SG .->BB res: 59 CYS at:SG . WARNING : link:SS is found dist = 2.042 ideal_dist= 2.031 ch:CC res: 3 CYS at:SG .->CC res: 21 CYS at:SG . WARNING : link:SS is found dist = 2.061 ideal_dist= 2.031 ch:CC res: 14 CYS at:SG .->CC res: 38 CYS at:SG . WARNING : link:SS is found dist = 2.053 ideal_dist= 2.031 ch:CC res: 42 CYS at:SG .->CC res: 53 CYS at:SG . WARNING : link:SS is found dist = 2.031 ideal_dist= 2.031 ch:CC res: 54 CYS at:SG .->CC res: 59 CYS at:SG . -------------------------------- --- title of input coord file --- PDB_code:XXXX PDB_name:---- PDB_date:XX-XXX-XX -------------------------------- WARNING : atom :HA LEU AA 1 is missing in the structure WARNING : atom :HB1 LEU AA 1 is missing in the structure WARNING : atom :HB2 LEU AA 1 is missing in the structure WARNING : atom :HG LEU AA 1 is missing in the structure WARNING : atom :HD11 LEU AA 1 is missing in the structure WARNING : atom :HD12 LEU AA 1 is missing in the structure WARNING : atom :HD13 LEU AA 1 is missing in the structure WARNING : atom :HD21 LEU AA 1 is missing in the structure WARNING : atom :HD22 LEU AA 1 is missing in the structure WARNING : atom :HD23 LEU AA 1 is missing in the structure WARNING : atom :H1 LEU AA 1 is missing in the structure WARNING : atom :H2 LEU AA 1 is missing in the structure WARNING : atom :H3 LEU AA 1 is missing in the structure WARNING : atom :HA LYS AA 2 is missing in the structure WARNING : atom :CB LYS AA 2 is missing in the structure WARNING : atom :HB1 LYS AA 2 is missing in the structure WARNING : atom :HB2 LYS AA 2 is missing in the structure WARNING : atom :CG LYS AA 2 is missing in the structure WARNING : atom :HG1 LYS AA 2 is missing in the structure WARNING : atom :HG2 LYS AA 2 is missing in the structure ... and more ... Number of chains : 3 Total number of monomers : 150 Number of atoms : 2427 Number of missing atoms : 1491 Number of rebuilt atoms : 834 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 0.8669 Number of reflections in file 23438 Number of reflection read 23438 CGMAT cycle number = 1 **** Chiral volume outliers **** Chiral volume deviations from the ideal >10.000Sigma will be monitored A 49 ILE CB mod.= -2.39 id.= 2.64 dev= 5.037 sig.= 0.200 B 49 ILE CB mod.= -2.39 id.= 2.64 dev= 5.030 sig.= 0.200 C 49 ILE CB mod.= -2.39 id.= 2.64 dev= 5.033 sig.= 0.200 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored C 48 LEU HB2 . - C 48 LEU HD21. mod.= 0.676 id.= 2.400 dev= -1.72 sig.= 0.20 sym.= 2 0 0 0 w_average 0.129877925 GRID VALUES: 0.0760869533 Angstrom for D 5.13333321 Angstrom^2 for B special position ----------- 2.6318593 special position ----------- 3.44163132 special position ----------- 3.27041411 special position ----------- 3.85336566 special position ----------- 3.26833391 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 954 0.017 0.021 Bond distances: others 777 0.000 0.020 Bond angles : refined atoms 1293 3.508 2.004 Bond angles : others 1764 4.790 3.000 Torsion angles, period 1. refined 141 0.359 5.000 Torsion angles, period 2. refined 21 28.866 24.286 Torsion angles, period 3. refined 105 23.387 15.000 Torsion angles, period 4. refined 3 24.286 15.000 Chiral centres: refined atoms 141 0.749 0.200 Planar groups: refined atoms 1119 0.002 0.020 Planar groups: others 168 0.001 0.020 VDW repulsions: refined atoms 133 0.197 0.200 VDW repulsions: others 706 0.276 0.200 VDW; torsion: refined atoms 411 0.186 0.200 VDW; torsion: others 526 0.157 0.200 HBOND: refined atoms 24 0.106 0.200 VDW repulsions; symmetry: refined atoms 8 0.483 0.200 VDW repulsions; symmetry: others 30 0.594 0.200 HBOND; symmetry: refined atoms 2 0.170 0.200 M. chain bond B values: refined atoms 714 0.000 1.500 M. chain bond B values: others 303 0.000 1.500 M. chain angle B values: refined atoms 1089 0.000 2.000 M. chain angle B values: others 918 0.000 2.000 S. chain bond B values: refined atoms 240 0.000 3.000 S. chain bond B values: others 474 0.000 3.000 S. chain angle B values: refined atoms 204 0.000 4.500 S. chain angle B values: others 846 0.000 4.500 NCS: tight positional , group 1 chain A 571 0.001 0.050 NCS: tight thermal , group 1 chain A 571 0.000 0.500 NCS: tight positional , group 1 chain B 571 0.001 0.050 NCS: tight thermal , group 1 chain B 571 0.000 0.500 NCS: tight positional , group 1 chain C 571 0.001 0.050 NCS: tight thermal , group 1 chain C 571 0.000 0.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 13.685, B = -0.406 Babinet"s bulk solvent: scale = 0.498, B = 165.879 Partial structure 1: scale = 0.330, B = 54.042 Overall anisotropic scale factors B11 = 0.23 B22 = 0.09 B33 = -0.52 B12 = 0.00 B13 = -0.22 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 1. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 1. v. resln :N:1,6,7,11,12: :Cycle 1. and v. resln :N:1,4,5,9,10: :Cycle 1. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.011 277 98.64 351.4 299.3 0.45 0.46 13 398.0 338.6 0.43 0.39 0.032 482 100.00 360.8 334.5 0.49 0.46 20 376.6 307.3 0.41 0.38 0.053 602 100.00 449.6 365.8 0.45 0.44 26 487.2 435.4 0.56 0.52 0.074 718 100.00 397.3 302.9 0.49 0.47 39 363.6 326.2 0.42 0.44 0.095 799 100.00 287.7 244.3 0.52 0.49 51 294.7 266.1 0.57 0.52 0.116 872 100.00 229.3 202.0 0.54 0.50 52 271.6 214.6 0.50 0.47 0.138 966 100.00 193.9 174.6 0.57 0.54 42 192.1 173.2 0.61 0.59 0.159 1010 100.00 184.6 152.3 0.51 0.48 61 168.8 139.8 0.45 0.43 0.180 1102 99.83 163.2 131.9 0.54 0.51 62 169.5 123.9 0.53 0.49 0.201 1104 95.72 147.4 115.7 0.54 0.52 59 148.4 119.6 0.59 0.55 0.222 998 83.68 135.9 106.2 0.54 0.51 53 139.6 118.2 0.54 0.52 0.243 892 71.43 122.0 91.9 0.54 0.51 53 115.8 96.8 0.55 0.52 0.264 916 68.62 101.0 79.0 0.55 0.51 31 104.4 84.4 0.52 0.51 0.285 907 65.79 85.8 67.8 0.55 0.52 39 85.0 66.3 0.56 0.55 0.306 905 64.96 74.6 57.9 0.54 0.53 57 64.4 56.5 0.51 0.52 0.327 902 61.69 68.0 49.0 0.53 0.54 53 70.7 52.5 0.59 0.62 0.349 843 57.01 60.8 43.0 0.51 0.52 64 60.0 39.3 0.54 0.55 0.370 772 50.34 54.4 39.1 0.53 0.55 40 46.9 40.6 0.44 0.47 0.391 731 45.56 48.2 34.4 0.50 0.51 39 49.1 38.5 0.58 0.61 0.412 459 27.85 41.8 31.9 0.46 0.49 15 36.2 32.1 0.37 0.38 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 1. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 1. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0110 219 0.544 58 0.578 277 0.551 0.661 0.0321 421 0.602 61 0.417 482 0.579 0.626 0.0532 539 0.658 63 0.603 602 0.652 0.599 0.0743 654 0.609 64 0.475 718 0.597 0.578 0.0954 738 0.491 61 0.248 799 0.473 0.559 0.1165 813 0.384 59 0.418 872 0.386 0.543 0.1376 901 0.333 65 0.281 966 0.329 0.528 0.1587 951 0.314 59 0.230 1010 0.309 0.514 0.1798 1039 0.281 63 0.227 1102 0.278 0.508 0.2009 1044 0.269 60 0.210 1104 0.266 0.507 0.2220 942 0.280 56 0.185 998 0.275 0.506 0.2431 826 0.281 66 0.183 892 0.274 0.510 0.2642 851 0.272 65 0.204 916 0.268 0.517 0.2853 844 0.259 63 0.237 907 0.257 0.507 0.3064 839 0.239 66 0.204 905 0.236 0.470 0.3275 843 0.239 59 0.237 902 0.239 0.449 0.3486 785 0.267 58 0.224 843 0.264 0.498 0.3697 713 0.296 59 0.213 772 0.290 0.539 0.3908 674 0.267 57 0.208 731 0.263 0.489 0.4119 423 0.234 36 0.165 459 0.229 0.430 $$ Resolution limits = 50.000 1.539 Number of used reflections = 16257 Percentage observed = 73.0725 Percentage of free reflections = 5.0742 Overall R factor = 0.5157 Free R factor = 0.5170 Overall weighted R factor = 0.4908 Free weighted R factor = 0.4899 Overall correlation coefficient = 0.6474 Free correlation coefficient = 0.6564 Cruickshanks DPI for coordinate error= 0.2451 DPI based on free R factor = 0.2156 Overall figure of merit = 0.3302 ML based su of positional parameters = 0.5190 ML based su of thermal parameters = 14.4989 ----------------------------------------------------------------------------- Trying gamma equal 0. Convergence reached with no gamma cycles CGMAT cycle number = 2 w_average 0.195761383 GRID VALUES: 0.0760869533 Angstrom for D 4.85294104 Angstrom^2 for B special position ----------- 2.89867759 special position ----------- 3.72792768 special position ----------- 3.46992183 special position ----------- 2.97626877 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 954 0.115 0.021 Bond distances: others 777 0.020 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 14.530, B = -0.838 Babinet"s bulk solvent: scale = 0.487, B = 105.532 Partial structure 1: scale = 0.338, B = 84.586 Overall anisotropic scale factors B11 = 0.23 B22 = 0.09 B33 = -0.52 B12 = 0.00 B13 = -0.22 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4549 Free R factor = 0.4873 Overall figure of merit = 0.4408 ----------------------------------------------------------------------------- Trying gamma equal 0. Convergence reached with no gamma cycles CGMAT cycle number = 3 w_average 0.21866405 GRID VALUES: 0.0760869533 Angstrom for D 5.02941179 Angstrom^2 for B special position ----------- 3.00566745 special position ----------- 3.80543399 special position ----------- 3.53262973 special position ----------- 2.99507046 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 954 0.079 0.021 Bond distances: others 777 0.012 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 14.462, B = -0.628 Babinet"s bulk solvent: scale = 0.494, B = 119.377 Partial structure 1: scale = 0.335, B = 77.689 Overall anisotropic scale factors B11 = 0.23 B22 = 0.09 B33 = -0.52 B12 = 0.00 B13 = -0.22 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4426 Free R factor = 0.4777 Overall figure of merit = 0.4799 ----------------------------------------------------------------------------- Trying gamma equal 0. Convergence reached with no gamma cycles CGMAT cycle number = 4 w_average 0.236255839 GRID VALUES: 0.0760869533 Angstrom for D 5.11764717 Angstrom^2 for B special position ----------- 3.06159353 special position ----------- 3.81315947 special position ----------- 3.52806568 special position ----------- 3.04315209 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 954 0.069 0.021 Bond distances: others 777 0.010 0.020 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 14.458, B = -0.363 Babinet"s bulk solvent: scale = 0.492, B = 127.681 Partial structure 1: scale = 0.334, B = 70.362 Overall anisotropic scale factors B11 = 0.23 B22 = 0.09 B33 = -0.52 B12 = 0.00 B13 = -0.22 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall R factor = 0.4322 Free R factor = 0.4695 Overall figure of merit = 0.5098 ----------------------------------------------------------------------------- Trying gamma equal 0. Convergence reached with no gamma cycles CGMAT cycle number = 5 **** Chiral volume outliers **** Chiral volume deviations from the ideal >10.000Sigma will be monitored A 49 ILE CB mod.= -0.36 id.= 2.64 dev= 3.002 sig.= 0.200 B 49 ILE CB mod.= -0.32 id.= 2.64 dev= 2.963 sig.= 0.200 C 49 ILE CB mod.= -0.75 id.= 2.64 dev= 3.391 sig.= 0.200 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored C 48 LEU HB2 . - C 48 LEU HD21. mod.= 0.911 id.= 2.400 dev= -1.49 sig.= 0.20 sym.= 2 0 0 0 **** NCS restraint outliers **** Deviations from the average position >10.000Sigma will be monitored Positional: B 25 THR O . deviation = 0.564 sigma= 0.050 Positional: B 27 ARG O . deviation = 0.880 sigma= 0.050 Positional: C 27 ARG O . deviation = 0.578 sigma= 0.050 Positional: A 34 VAL O . deviation = 0.520 sigma= 0.050 Positional: B 57 ASP OD1 . deviation = 0.506 sigma= 0.050 w_average 0.24952285 GRID VALUES: 0.0760869533 Angstrom for D 4.88888884 Angstrom^2 for B special position ----------- 3.11740661 special position ----------- 3.77491307 special position ----------- 3.50256491 special position ----------- 3.12718606 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 954 0.062 0.021 Bond distances: others 777 0.010 0.020 Bond angles : refined atoms 1293 4.685 2.004 Bond angles : others 1764 3.172 3.000 Torsion angles, period 1. refined 141 10.163 5.000 Torsion angles, period 2. refined 21 27.808 24.286 Torsion angles, period 3. refined 105 24.871 15.000 Torsion angles, period 4. refined 3 34.993 15.000 Chiral centres: refined atoms 141 0.541 0.200 Planar groups: refined atoms 1119 0.023 0.020 Planar groups: others 168 0.011 0.020 VDW repulsions: refined atoms 132 0.194 0.200 VDW repulsions: others 649 0.252 0.200 VDW; torsion: refined atoms 363 0.232 0.200 VDW; torsion: others 594 0.128 0.200 HBOND: refined atoms 13 0.281 0.200 HBOND: others 1 0.013 0.200 VDW repulsions; symmetry: refined atoms 5 0.528 0.200 VDW repulsions; symmetry: others 26 0.566 0.200 M. chain bond B values: refined atoms 761 2.110 1.500 M. chain bond B values: others 303 1.255 1.500 M. chain angle B values: refined atoms 1089 2.363 2.000 M. chain angle B values: others 918 1.501 2.000 S. chain bond B values: refined atoms 256 3.966 3.000 S. chain bond B values: others 522 2.668 3.000 S. chain angle B values: refined atoms 204 3.883 4.500 S. chain angle B values: others 846 2.677 4.500 NCS: tight positional , group 1 chain A 571 0.169 0.050 NCS: tight thermal , group 1 chain A 571 0.807 0.500 NCS: tight positional , group 1 chain B 571 0.166 0.050 NCS: tight thermal , group 1 chain B 571 0.762 0.500 NCS: tight positional , group 1 chain C 571 0.155 0.050 NCS: tight thermal , group 1 chain C 571 0.749 0.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 14.539, B = -0.226 Babinet"s bulk solvent: scale = 0.476, B = 126.598 Partial structure 1: scale = 0.342, B = 70.520 Overall anisotropic scale factors B11 = 0.23 B22 = 0.09 B33 = -0.52 B12 = 0.00 B13 = -0.22 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 5. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 5. v. resln :N:1,6,7,11,12: :Cycle 5. and v. resln :N:1,4,5,9,10: :Cycle 5. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.011 277 98.64 330.8 285.3 0.43 0.45 13 374.6 302.9 0.41 0.35 0.032 482 100.00 339.7 326.2 0.43 0.41 20 354.5 321.3 0.43 0.39 0.053 602 100.00 423.2 368.1 0.37 0.37 26 458.5 404.1 0.56 0.54 0.074 718 100.00 373.9 317.7 0.39 0.38 39 342.3 278.7 0.36 0.36 0.095 799 100.00 270.8 240.9 0.42 0.39 51 277.4 245.2 0.49 0.44 0.116 872 100.00 215.9 198.0 0.47 0.44 52 255.6 219.1 0.45 0.45 0.138 966 100.00 182.5 167.1 0.48 0.46 42 180.8 170.5 0.47 0.47 0.159 1010 100.00 173.8 154.6 0.42 0.41 61 158.9 128.9 0.53 0.50 0.180 1102 99.83 153.6 134.7 0.45 0.43 62 159.5 137.5 0.34 0.30 0.201 1104 95.72 138.7 117.6 0.45 0.43 59 139.7 126.4 0.48 0.44 0.222 998 83.68 127.9 110.7 0.43 0.40 53 131.4 117.3 0.56 0.51 0.243 892 71.43 114.8 94.4 0.43 0.40 53 109.0 95.8 0.48 0.43 0.264 916 68.62 95.1 83.5 0.44 0.40 31 98.3 87.6 0.47 0.46 0.285 907 65.79 80.8 72.1 0.43 0.41 39 80.1 74.1 0.44 0.43 0.306 905 64.96 70.2 60.6 0.42 0.40 57 60.6 57.9 0.40 0.38 0.327 902 61.69 64.0 55.6 0.38 0.37 53 66.6 53.3 0.51 0.55 0.349 843 57.01 57.2 45.8 0.41 0.40 64 56.5 45.6 0.45 0.46 0.370 772 50.34 51.2 43.1 0.38 0.37 40 44.2 39.7 0.46 0.47 0.391 731 45.56 45.4 37.7 0.39 0.40 39 46.2 42.2 0.51 0.50 0.412 459 27.85 39.3 35.6 0.36 0.36 15 34.1 33.7 0.52 0.54 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 5. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 5. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0110 219 0.618 58 0.656 277 0.626 0.740 0.0321 421 0.695 61 0.520 482 0.672 0.739 0.0532 539 0.757 63 0.656 602 0.746 0.738 0.0743 654 0.734 64 0.570 718 0.719 0.737 0.0954 738 0.634 61 0.348 799 0.612 0.736 0.1165 813 0.539 59 0.515 872 0.538 0.736 0.1376 901 0.499 65 0.436 966 0.495 0.735 0.1587 951 0.514 59 0.388 1010 0.506 0.735 0.1798 1039 0.487 63 0.396 1102 0.482 0.750 0.2009 1044 0.483 60 0.413 1104 0.479 0.771 0.2220 942 0.519 56 0.386 998 0.512 0.789 0.2431 826 0.522 66 0.330 892 0.508 0.800 0.2642 851 0.524 65 0.440 916 0.518 0.808 0.2853 844 0.521 63 0.435 907 0.515 0.804 0.3064 839 0.498 66 0.420 905 0.492 0.782 0.3275 843 0.518 59 0.529 902 0.519 0.768 0.3486 785 0.499 58 0.422 843 0.494 0.791 0.3697 713 0.530 59 0.429 772 0.522 0.805 0.3908 674 0.491 57 0.384 731 0.483 0.740 0.4119 423 0.450 36 0.312 459 0.439 0.670 $$ Resolution limits = 50.000 1.539 Number of used reflections = 16257 Percentage observed = 73.0725 Percentage of free reflections = 5.0742 Overall R factor = 0.4245 Free R factor = 0.4610 Overall weighted R factor = 0.4075 Free weighted R factor = 0.4359 Overall correlation coefficient = 0.7640 Free correlation coefficient = 0.7117 Cruickshanks DPI for coordinate error= 0.2018 DPI based on free R factor = 0.1923 Overall figure of merit = 0.5329 ML based su of positional parameters = 0.1791 ML based su of thermal parameters = 4.8239 ----------------------------------------------------------------------------- Trying gamma equal 0. Convergence reached with no gamma cycles **** Chiral volume outliers **** Chiral volume deviations from the ideal >10.000Sigma will be monitored A 49 ILE CB mod.= 0.10 id.= 2.64 dev= 2.548 sig.= 0.200 B 49 ILE CB mod.= 0.15 id.= 2.64 dev= 2.499 sig.= 0.200 C 49 ILE CB mod.= -0.13 id.= 2.64 dev= 2.777 sig.= 0.200 **** VDW outliers **** VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored C 48 LEU HB2 . - C 48 LEU HD21. mod.= 0.928 id.= 2.400 dev= -1.47 sig.= 0.20 sym.= 2 0 0 0 **** NCS restraint outliers **** Deviations from the average position >10.000Sigma will be monitored Positional: B 25 THR O . deviation = 0.562 sigma= 0.050 Positional: B 27 ARG O . deviation = 0.845 sigma= 0.050 Positional: C 27 ARG O . deviation = 0.563 sigma= 0.050 Positional: B 57 ASP OD1 . deviation = 0.522 sigma= 0.050 WRITTEN OUTPUT MTZ FILE Logical Name: HKLOUT Filename: /y/people/mgwt/work/2003test_182_4_mtz_1.tmp * Title: Output mtz file from refmac * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 0 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: * Number of Columns = 13 * Number of Reflections = 23433 * Missing value set to NaN in input mtz file * HISTORY for current MTZ file : * Column Labels, Types, Ranges [and Dataset IDs] : H H -51.0000 45.0000 0 K H 0.0000 26.0000 0 L H 0.0000 36.0000 0 F F 11.5120 1439.8521 0 SIGF Q 1.4355 32.5872 0 FreeR_flag I 0.0000 19.0000 0 FC F 0.4158 5185.5029 0 PHIC P 0.0000 360.0000 0 FWT F 0.0055 1714.0000 0 PHWT P 0.0000 360.0000 0 DELFWT F 0.0000 722.1420 0 PHDELWT P 0.0000 360.0000 0 FOM W 0.0000 1.0000 0 * Cell Dimensions : (obsolete - use crystal cells) 78.7000 40.4000 56.0000 90.0000 117.1000 90.0000 * Resolution Range : 0.00096 0.42228 ( 32.310 - 1.539 A ) * Sort Order : 1 2 3 0 0 * Number of Symmetry Operations = 4 * Number of Primitive Operations = 2 * Space Group = 5 C2 * Lattice Type = C * Point Group Name = PG2 * Symmetry Operations : Symmetry 1 X, Y, Z 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 Symmetry 2 -X, Y, -Z -1.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 -1.00 0.00 0.00 0.00 0.00 1.00 Symmetry 3 X+1/2, Y+1/2, Z 1.00 0.00 0.00 0.50 0.00 1.00 0.00 0.50 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00 Symmetry 4 -X+1/2, Y+1/2, -Z -1.00 0.00 0.00 0.50 0.00 1.00 0.00 0.50 0.00 0.00 -1.00 0.00 0.00 0.00 0.00 1.00 special position ----------- 3.18128085 special position ----------- 3.71337104 special position ----------- 3.48271799 special position ----------- 3.235991 ------------------------------------------------------------------------------- Restraint type N restraints Rms Delta Av(Sigma) Bond distances: refined atoms 954 0.057 0.021 Bond distances: others 777 0.009 0.020 Bond angles : refined atoms 1293 4.458 2.004 Bond angles : others 1764 3.103 3.000 Torsion angles, period 1. refined 141 10.176 5.000 Torsion angles, period 2. refined 21 28.460 24.286 Torsion angles, period 3. refined 105 24.766 15.000 Torsion angles, period 4. refined 3 35.154 15.000 Chiral centres: refined atoms 141 0.469 0.200 Planar groups: refined atoms 1119 0.021 0.020 Planar groups: others 168 0.011 0.020 VDW repulsions: refined atoms 125 0.200 0.200 VDW repulsions: others 645 0.249 0.200 VDW; torsion: refined atoms 371 0.221 0.200 VDW; torsion: others 578 0.125 0.200 HBOND: refined atoms 11 0.322 0.200 VDW repulsions; symmetry: refined atoms 5 0.513 0.200 VDW repulsions; symmetry: others 26 0.555 0.200 M. chain bond B values: refined atoms 760 1.996 1.500 M. chain bond B values: others 303 1.166 1.500 M. chain angle B values: refined atoms 1089 2.291 2.000 M. chain angle B values: others 918 1.429 2.000 S. chain bond B values: refined atoms 258 3.935 3.000 S. chain bond B values: others 524 2.722 3.000 S. chain angle B values: refined atoms 204 3.840 4.500 S. chain angle B values: others 846 2.716 4.500 NCS: tight positional , group 1 chain A 571 0.168 0.050 NCS: tight thermal , group 1 chain A 571 0.736 0.500 NCS: tight positional , group 1 chain B 571 0.160 0.050 NCS: tight thermal , group 1 chain B 571 0.693 0.500 NCS: tight positional , group 1 chain C 571 0.150 0.050 NCS: tight thermal , group 1 chain C 571 0.690 0.500 ------------------------------------------------------------------------------- ----------------------------------------------------------------------------- Overall : scale = 14.647, B = -0.159 Babinet"s bulk solvent: scale = 0.476, B = 125.525 Partial structure 1: scale = 0.343, B = 69.798 Overall anisotropic scale factors B11 = 0.23 B22 = 0.09 B33 = -0.52 B12 = 0.00 B13 = -0.22 B23 = 0.00 ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- **** Things for loggraph, R factor and others **** $TABLE: Cycle 6. Rfactor analysis, F distribution v resln : $GRAPHS:Cycle 6. v. resln :N:1,6,7,11,12: :Cycle 6. and v. resln :N:1,4,5,9,10: :Cycle 6. % observed v. resln :N:1,3: $$ M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$ $$ 0.011 277 98.64 328.3 284.4 0.43 0.44 13 371.8 300.2 0.41 0.35 0.032 482 100.00 337.1 325.0 0.43 0.41 20 351.8 320.4 0.43 0.40 0.053 602 100.00 420.1 364.5 0.37 0.37 26 455.1 398.4 0.55 0.53 0.074 718 100.00 371.2 315.8 0.39 0.38 39 339.7 278.5 0.35 0.36 0.095 799 100.00 268.8 240.2 0.41 0.39 51 275.3 242.7 0.48 0.43 0.116 872 100.00 214.3 198.2 0.46 0.43 52 253.7 221.2 0.44 0.44 0.138 966 100.00 181.1 166.6 0.47 0.45 42 179.5 171.8 0.45 0.46 0.159 1010 100.00 172.5 154.6 0.42 0.40 61 157.7 128.7 0.52 0.50 0.180 1102 99.83 152.5 134.9 0.44 0.42 62 158.3 138.4 0.35 0.31 0.201 1104 95.72 137.7 117.8 0.44 0.42 59 138.7 126.8 0.47 0.43 0.222 998 83.68 126.9 110.3 0.42 0.39 53 130.4 117.2 0.55 0.50 0.243 892 71.43 114.0 94.5 0.41 0.39 53 108.2 96.2 0.46 0.41 0.264 916 68.62 94.4 83.5 0.42 0.39 31 97.6 87.7 0.45 0.44 0.285 907 65.79 80.2 71.7 0.42 0.39 39 79.5 74.1 0.43 0.42 0.306 905 64.96 69.7 60.4 0.41 0.39 57 60.2 58.1 0.39 0.38 0.327 902 61.69 63.5 55.7 0.37 0.36 53 66.1 52.3 0.51 0.55 0.349 843 57.01 56.8 45.7 0.40 0.39 64 56.1 45.0 0.43 0.44 0.370 772 50.34 50.8 43.2 0.37 0.35 40 43.9 39.4 0.45 0.44 0.391 731 45.56 45.0 37.8 0.38 0.38 39 45.9 41.8 0.48 0.46 0.412 459 27.85 39.0 35.5 0.35 0.35 15 33.8 32.7 0.49 0.51 $$ **** Fom and SigmaA vs resolution **** $TABLE: Cycle 6. Fom(-acentric, centric, overall v resln: $GRAPHS:Cycle 6. M(Fom) v. resln :N:1,3,5,7,8: $$ <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$ $$ 0.0110 219 0.627 58 0.662 277 0.634 0.748 0.0321 421 0.703 61 0.532 482 0.681 0.749 0.0532 539 0.763 63 0.657 602 0.752 0.749 0.0743 654 0.743 64 0.587 718 0.729 0.749 0.0954 738 0.646 61 0.365 799 0.624 0.750 0.1165 813 0.556 59 0.527 872 0.554 0.750 0.1376 901 0.515 65 0.451 966 0.511 0.750 0.1587 951 0.531 59 0.414 1010 0.524 0.751 0.1798 1039 0.505 63 0.414 1102 0.500 0.766 0.2009 1044 0.502 60 0.431 1104 0.498 0.787 0.2220 942 0.534 56 0.406 998 0.527 0.805 0.2431 826 0.543 66 0.345 892 0.529 0.820 0.2642 851 0.550 65 0.477 916 0.544 0.832 0.2853 844 0.551 63 0.472 907 0.545 0.829 0.3064 839 0.521 66 0.435 905 0.515 0.802 0.3275 843 0.535 59 0.541 902 0.535 0.784 0.3486 785 0.515 58 0.447 843 0.510 0.808 0.3697 713 0.552 59 0.454 772 0.544 0.823 0.3908 674 0.523 57 0.409 731 0.514 0.768 0.4119 423 0.488 36 0.324 459 0.475 0.708 $$ Resolution limits = 50.000 1.539 Number of used reflections = 16257 Percentage observed = 73.0725 Percentage of free reflections = 5.0742 Overall R factor = 0.4178 Free R factor = 0.4524 Overall weighted R factor = 0.4018 Free weighted R factor = 0.4274 Overall correlation coefficient = 0.7693 Free correlation coefficient = 0.7205 Cruickshanks DPI for coordinate error= 0.1986 DPI based on free R factor = 0.1887 Overall figure of merit = 0.5517 ML based su of positional parameters = 0.1791 ML based su of thermal parameters = 4.8239 ----------------------------------------------------------------------------- Time in seconds: CPU = 40.79 Elapsed = 41.00 **** Things for loggraph, R factor and others vs cycle **** $TABLE: Rfactor analysis, stats vs cycle : $GRAPHS: vs cycle :N:1,2,3: :FOM vs cycle :N:1,4: :-LLG vs cycle :N:1,5: :Geometry vs cycle:N:1,6,7,8: $$ Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$ $$ 0 0.516 0.517 0.330 96278.5 0.017 3.508 0.749 1 0.455 0.487 0.441 94058.7 0.115 6.938 0.787 2 0.443 0.478 0.480 93771.6 0.079 5.295 0.681 3 0.432 0.470 0.510 93447.4 0.069 4.972 0.616 4 0.424 0.461 0.533 93104.9 0.062 4.685 0.541 5 0.418 0.452 0.552 92764.8 0.057 4.458 0.469 $$ Harvest: NO PNAME_KEYWRD given - no deposit file created Refmac_5.1.9999: End of Refmac_5.1.9999 Times: User: 45.8s System: 1.7s Elapsed: 0:48 *************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final coordinates to /y/people/mgwt/TEST/model_molrep2_refmac1.pdb *************************************************************************** *************************************************************************** * Information from CCP4Interface script *************************************************************************** Writing final phases to /y/people/mgwt/TEST/cardiotoxin_refmac1.mtz *************************************************************************** #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 19 Sep 2003 14:59:13 #CCP4I MESSAGE Task completed successfully