Summary:
| Initial | After 5 cycles | |
|---|---|---|
| R factor | 0.228 | 0.155 |
| Rfree | 0.221 | 0.190 |
| RMSD Bond Length | 0.028 | 0.031 |
| RMSD Bond Angle | 4.533 | 2.378 |
| RMSD Chiral Centre | 0.163 | 0.202 |
|
The following tables were found in the logfile: Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 5. Rfactor analysis, F distribution v resln Cycle 5. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 6. Rfactor analysis, F distribution v resln Cycle 6. Fom(<cos(DelPhi)>-acentric, centric, overall v resln |
Cycle 1. Rfactor analysis, F distribution v resln Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 5. Rfactor analysis, F distribution v resln Cycle 5. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 6. Rfactor analysis, F distribution v resln Cycle 6. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Rfactor analysis, stats vs cycle |
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
############################################################### ############################################################### ############################################################### ### CCP4 6.0: Refmac_5.3.0040 version 5.3.0040 : 12/07/07## ############################################################### User: pjx Run date: 17/ 7/2007 Run time: 11:42:19 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
MAKE
Data line--- make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
MAKE
Data line--- refi type REST resi MLKF meth CGMAT bref ISOT
REFI
Data line--- ncyc 5
NCYC
Data line--- scal type SIMP reso 1.833 50.000 LSSC ANISO EXPE
SCAL
Data line--- solvent YES VDWProb 1.2 IONProb 0.8 RSHRink 0.8
SOLV
Data line--- weight AUTO
WEIG
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
MONI
Data line--- labin FP=FNAT SIGFP=SIGFNAT FREE=FreeR_flag
LABI
Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM
LABO
Data line--- PNAME RNASE
PNAM
Data line--- DNAME NATIVE
DNAM
Data line--- RSIZE 80
RSIZ
Data line--- END
END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /home/pjx/CCP4_REMOTE/ccp4/examples/rnase/rnase18.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name - /home/pjx/CCP4_REMOTE/ccp4/examples/rnase/rnase.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /tmp/pjx/PROJECT_156_2_pdb_1.tmp
Input reflection file. Logical name - HKLIN actual file name - /home/pjx/CCP4_REMOTE/ccp4/examples/rnase/rnase18.mtz
Output reflection file. Logical name - HKLOUT actual file name - /tmp/pjx/PROJECT_156_3_mtz_1.tmp
Cell from mtz : 64.897 78.323 38.792 90.000 90.000 90.000
Space group from mtz: number - 19; name - P 21 21 21
Refinement type : Restrained
**** Makecif parameters ****
Dictionary files for restraints : /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/pjx/CCP4I_uWORKSHOP/ccp4/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 in input coordinate file will be kept
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
Method of minimisation : Sparse Matrix
Experimental sigmas used for weighting
Number of Bins and width: 20 0.0149
Refinement of individual isotropic Bfactors
Refinement resln : 50.0000 1.8330
Estimated number of reflections : 23839
Free R exclusion - flag equals: 0
Auto weighting. An attempt
Refinement cycles : 5
Scaling type :
Wilson using 1 Gaussian
using working set of reflns and 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 1.8330
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
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
---------------------------------------------------------------
Input file :/home/pjx/CCP4_REMOTE/ccp4/examples/rnase/rnase.pdb
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.30
_lib_update 02/03/07
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2433
with complete description : 450
NUMBER OF MODIFICATIONS : 47
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, Filename: /home/pjx/CCP4I_uWORKSHOP/ccp4/lib/data/atomsf.lib
Number of atoms : 1725
Number of residues : 417
Number of chains : 5
I am reading library. Please wait.
mon_lib.cif
WARNING : CIS peptide bond is found, angle = 3.78
ch:AA res: 26 GLY --> 27 PRO
WARNING : CIS peptide bond is found, angle = 0.13
ch:BB res: 26 GLY --> 27 PRO
WARNING : link:SS is found dist = 1.959 ideal_dist= 2.031
ch:AA res: 7 CYS at:SG .->AA res: 96 CYS at:SG .
WARNING : link:SS is found dist = 2.042 ideal_dist= 2.031
ch:BB res: 7 CYS at:SG .->BB res: 96 CYS at:SG .
--------------------------------
--- title of input coord file ---
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-XX
--------------------------------
Number of chains : 5
Total number of monomers : 417
Number of atoms : 1725
Number of missing atoms : 0
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0
Number of bonds restraints : 1538
Number of angles restraints : 2108
Number of torsions restraints : 1036
Number of chiralities : 234
Number of planar groups : 278
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
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 17991
Number of reflection read 17980
CGMAT cycle number = 1
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
B 75 ALA C . - B 76 THR N . mod.= 1.564 id.= 1.329 dev= -0.235 sig.= 0.014
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 40 ARG CD - A 40 ARG CZ mod.= 163.02 id.= 124.20 dev=-38.819 sig.= 1.500
A 54 GLU CA - A 54 GLU CG mod.= 146.91 id.= 114.10 dev=-32.813 sig.= 2.000
B 3 SER CA - B 3 SER OG mod.= 89.21 id.= 111.10 dev= 21.890 sig.= 2.000
B 40 ARG CA - B 40 ARG CG mod.= 151.13 id.= 114.10 dev=-37.029 sig.= 2.000
B 40 ARG CD - B 40 ARG CZ mod.= 156.99 id.= 124.20 dev=-32.795 sig.= 1.500
**** B-value outliers ****
B-value differences > 10.00Sigma will be monitored
A 1 ASP CG - A 1 ASP CA ABS(DELTA)= 20.840 Sigma= 2.000
A 25 ASP CG - A 25 ASP CA ABS(DELTA)= 24.000 Sigma= 2.000
B 5 THR CB - B 5 THR CA ABS(DELTA)= 15.830 Sigma= 1.500
weigth matrix 0.8005419
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.028 0.022
Bond angles : refined atoms 2108 4.533 1.964
Torsion angles, period 1. refined 190 3.891 5.000
Torsion angles, period 2. refined 74 31.700 23.784
Torsion angles, period 3. refined 216 14.007 15.000
Torsion angles, period 4. refined 10 21.347 15.000
Chiral centres: refined atoms 234 0.163 0.200
Planar groups: refined atoms 1212 0.016 0.020
VDW repulsions: refined atoms 624 0.239 0.200
VDW; torsion: refined atoms 1067 0.317 0.200
HBOND: refined atoms 121 0.179 0.200
VDW repulsions; symmetry: refined atoms 47 0.212 0.200
HBOND; symmetry: refined atoms 27 0.394 0.200
M. chain bond B values: refined atoms 956 3.209 1.500
M. chain angle B values: refined atoms 1558 4.517 2.000
S. chain bond B values: refined atoms 582 4.562 3.000
S. chain angle B values: refined atoms 550 6.301 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.845, B = 1.075
Partial structure 1: scale = 0.299, B = 27.184
Overall anisotropic scale factors
B11 = -0.57 B22 = 0.42 B33 = 0.15 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. 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.008 243 100.00 359.9 361.6 0.21 0.25 10 336.0 324.8 0.13 0.17
0.023 384 100.00 281.6 287.1 0.20 0.25 21 274.3 296.7 0.24 0.31
0.038 477 100.00 314.7 310.3 0.17 0.21 28 308.0 317.3 0.14 0.20
0.052 544 96.62 346.7 340.7 0.16 0.21 27 408.9 408.4 0.13 0.15
0.067 612 98.32 317.3 309.0 0.18 0.23 33 304.9 271.8 0.21 0.26
0.082 676 99.58 302.8 286.0 0.18 0.22 41 289.4 251.3 0.20 0.22
0.097 737 99.87 256.5 243.3 0.21 0.23 38 277.5 262.6 0.17 0.20
0.112 771 99.64 210.7 201.5 0.21 0.23 53 214.1 199.0 0.24 0.25
0.127 831 99.77 181.9 173.2 0.24 0.25 44 208.8 184.7 0.24 0.27
0.142 868 99.78 164.7 158.2 0.25 0.25 47 149.3 148.1 0.26 0.25
0.156 940 99.60 153.8 147.9 0.25 0.26 51 136.2 131.6 0.25 0.23
0.171 934 99.20 134.6 129.4 0.25 0.24 60 128.3 125.0 0.23 0.23
0.186 995 99.15 127.1 121.9 0.26 0.25 55 123.8 120.3 0.22 0.23
0.201 1029 99.00 119.8 113.5 0.25 0.24 58 122.1 122.5 0.23 0.22
0.216 1043 98.30 114.7 106.6 0.27 0.25 55 96.0 97.6 0.32 0.30
0.231 1083 97.76 101.5 97.7 0.27 0.25 53 100.2 93.2 0.26 0.25
0.246 1132 97.54 96.7 92.3 0.27 0.25 59 103.1 103.0 0.24 0.23
0.260 1128 96.73 85.9 84.5 0.28 0.26 54 84.0 84.5 0.24 0.21
0.275 1144 93.70 73.7 75.8 0.30 0.26 61 72.1 72.0 0.33 0.28
0.290 758 61.35 59.1 70.9 0.43 0.35 34 54.1 66.7 0.49 0.38
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0078 131 0.917 112 0.808 243 0.867 1.021
0.0227 270 0.869 114 0.776 384 0.842 1.014
0.0375 359 0.898 118 0.824 477 0.880 1.008
0.0524 438 0.935 106 0.828 544 0.914 1.001
0.0673 500 0.931 112 0.850 612 0.916 0.994
0.0821 565 0.931 111 0.852 676 0.918 0.988
0.0970 623 0.905 114 0.836 737 0.894 0.981
0.1118 657 0.895 114 0.812 771 0.883 0.975
0.1267 717 0.881 114 0.789 831 0.868 0.968
0.1416 759 0.856 109 0.812 868 0.850 0.962
0.1564 823 0.864 117 0.812 940 0.857 0.955
0.1713 825 0.854 109 0.766 934 0.843 0.949
0.1861 882 0.854 113 0.750 995 0.842 0.943
0.2010 919 0.853 110 0.787 1029 0.846 0.936
0.2158 936 0.846 107 0.814 1043 0.843 0.930
0.2307 982 0.841 101 0.751 1083 0.832 0.924
0.2456 1021 0.843 111 0.778 1132 0.837 0.918
0.2604 1032 0.828 96 0.743 1128 0.821 0.912
0.2753 1046 0.809 98 0.731 1144 0.803 0.906
0.2901 719 0.777 39 0.816 758 0.779 0.900
$$
Resolution limits = 50.000 1.833
Number of used reflections = 16329
Percentage observed = 95.7230
Percentage of free reflections = 5.1246
Overall R factor = 0.2283
Free R factor = 0.2206
Overall weighted R factor = 0.2396
Free weighted R factor = 0.2345
Overall correlation coefficient = 0.9305
Free correlation coefficient = 0.9326
Cruickshanks DPI for coordinate error= 0.1848
DPI based on free R factor = 0.1358
Overall figure of merit = 0.8510
ML based su of positional parameters = 0.0941
ML based su of thermal parameters = 3.1376
-----------------------------------------------------------------------------
Trying gamma equal 0.000000
Convergence reached with no gamma cycles
CGMAT cycle number = 2
weigth matrix 1.099140
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.029 0.022
Bond angles : refined atoms 2108 2.509 1.964
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.847, B = -0.159
Partial structure 1: scale = 0.299, B = 24.114
Overall anisotropic scale factors
B11 = -0.57 B22 = 0.42 B33 = 0.15 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1843
Free R factor = 0.2013
Overall figure of merit = 0.8721
-----------------------------------------------------------------------------
Trying gamma equal 0.000000
Convergence reached with no gamma cycles
CGMAT cycle number = 3
weigth matrix 1.204761
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.030 0.022
Bond angles : refined atoms 2108 2.448 1.964
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.850, B = -0.013
Partial structure 1: scale = 0.300, B = 21.474
Overall anisotropic scale factors
B11 = -0.57 B22 = 0.42 B33 = 0.15 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1689
Free R factor = 0.1951
Overall figure of merit = 0.8775
-----------------------------------------------------------------------------
Trying gamma equal 0.000000
Convergence reached with no gamma cycles
CGMAT cycle number = 4
weigth matrix 1.239633
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.031 0.022
Bond angles : refined atoms 2108 2.431 1.964
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.851, B = 0.003
Partial structure 1: scale = 0.300, B = 20.537
Overall anisotropic scale factors
B11 = -0.57 B22 = 0.42 B33 = 0.15 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1616
Free R factor = 0.1929
Overall figure of merit = 0.8790
-----------------------------------------------------------------------------
Trying gamma equal 0.000000
Convergence reached with no gamma cycles
CGMAT cycle number = 5
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 54 GLU CA - A 54 GLU CG mod.= 137.78 id.= 114.10 dev=-23.675 sig.= 2.000
weigth matrix 1.248353
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.031 0.022
Bond angles : refined atoms 2108 2.404 1.964
Torsion angles, period 1. refined 190 6.167 5.000
Torsion angles, period 2. refined 74 29.023 23.784
Torsion angles, period 3. refined 216 13.599 15.000
Torsion angles, period 4. refined 10 17.672 15.000
Chiral centres: refined atoms 234 0.202 0.200
Planar groups: refined atoms 1212 0.013 0.020
VDW repulsions: refined atoms 625 0.221 0.200
VDW; torsion: refined atoms 1078 0.315 0.200
HBOND: refined atoms 135 0.153 0.200
VDW repulsions; symmetry: refined atoms 49 0.154 0.200
HBOND; symmetry: refined atoms 27 0.345 0.200
M. chain bond B values: refined atoms 970 1.781 1.500
M. chain angle B values: refined atoms 1558 2.722 2.000
S. chain bond B values: refined atoms 629 4.183 3.000
S. chain angle B values: refined atoms 550 6.406 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.852, B = -0.002
Partial structure 1: scale = 0.300, B = 20.334
Overall anisotropic scale factors
B11 = -0.57 B22 = 0.42 B33 = 0.15 B12 = 0.00 B13 = 0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.008 243 100.00 357.1 359.0 0.19 0.23 10 333.4 322.2 0.19 0.23
0.023 384 100.00 279.4 292.0 0.17 0.21 21 272.1 300.3 0.20 0.28
0.038 477 100.00 312.2 313.3 0.13 0.17 28 305.6 323.8 0.14 0.20
0.052 544 96.62 344.0 338.7 0.12 0.15 27 405.7 398.3 0.11 0.14
0.067 612 98.32 314.9 305.7 0.13 0.16 33 302.5 278.8 0.14 0.18
0.082 676 99.58 300.4 285.2 0.14 0.16 41 287.1 260.8 0.19 0.23
0.097 737 99.87 254.6 241.7 0.15 0.16 38 275.3 253.6 0.17 0.20
0.112 771 99.64 209.0 201.4 0.15 0.16 53 212.4 195.8 0.20 0.21
0.127 831 99.77 180.5 175.4 0.17 0.18 44 207.2 190.5 0.18 0.21
0.142 868 99.78 163.5 159.8 0.17 0.18 47 148.1 150.2 0.22 0.23
0.156 940 99.60 152.6 148.9 0.17 0.17 51 135.1 136.3 0.17 0.18
0.171 934 99.20 133.6 131.3 0.17 0.17 60 127.3 123.4 0.24 0.24
0.186 995 99.15 126.1 124.0 0.17 0.16 55 122.9 123.8 0.22 0.22
0.201 1029 99.00 118.9 115.5 0.16 0.15 58 121.2 116.3 0.22 0.21
0.216 1043 98.30 113.8 110.2 0.16 0.15 55 95.3 97.9 0.23 0.22
0.231 1083 97.76 100.7 100.0 0.17 0.16 53 99.4 92.4 0.21 0.20
0.246 1132 97.54 96.0 94.7 0.16 0.15 59 102.3 105.9 0.23 0.22
0.260 1128 96.73 85.3 86.7 0.18 0.16 54 83.3 86.0 0.20 0.18
0.275 1144 93.70 73.2 75.8 0.18 0.16 61 71.6 78.1 0.25 0.22
0.290 758 61.35 58.7 69.4 0.30 0.24 34 53.7 71.4 0.43 0.29
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0078 131 0.937 112 0.832 243 0.889 1.020
0.0227 270 0.901 114 0.811 384 0.874 1.015
0.0375 359 0.915 118 0.855 477 0.900 1.010
0.0524 438 0.946 106 0.894 544 0.936 1.004
0.0673 500 0.946 112 0.850 612 0.928 0.999
0.0821 565 0.942 111 0.866 676 0.929 0.994
0.0970 623 0.926 114 0.870 737 0.917 0.989
0.1118 657 0.916 114 0.838 771 0.905 0.984
0.1267 717 0.900 114 0.836 831 0.891 0.979
0.1416 759 0.886 109 0.827 868 0.879 0.974
0.1564 823 0.888 117 0.831 940 0.881 0.969
0.1713 825 0.880 109 0.803 934 0.871 0.964
0.1861 882 0.882 113 0.787 995 0.871 0.959
0.2010 919 0.878 110 0.859 1029 0.876 0.954
0.2158 936 0.880 107 0.811 1043 0.873 0.949
0.2307 982 0.870 101 0.780 1083 0.861 0.944
0.2456 1021 0.878 111 0.816 1132 0.872 0.939
0.2604 1032 0.863 96 0.813 1128 0.859 0.935
0.2753 1046 0.844 98 0.773 1144 0.838 0.930
0.2901 719 0.824 39 0.847 758 0.826 0.926
$$
Resolution limits = 50.000 1.833
Number of used reflections = 16329
Percentage observed = 95.7230
Percentage of free reflections = 5.1246
Overall R factor = 0.1579
Free R factor = 0.1915
Overall weighted R factor = 0.1682
Free weighted R factor = 0.2089
Overall correlation coefficient = 0.9643
Free correlation coefficient = 0.9497
Cruickshanks DPI for coordinate error= 0.1278
DPI based on free R factor = 0.1178
Overall figure of merit = 0.8792
ML based su of positional parameters = 0.0754
ML based su of thermal parameters = 2.4975
-----------------------------------------------------------------------------
Trying gamma equal 0.000000
Convergence reached with no gamma cycles
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 54 GLU CA - A 54 GLU CG mod.= 137.04 id.= 114.10 dev=-22.943 sig.= 2.000
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /tmp/pjx/PROJECT_156_3_mtz_1.tmp
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.031 0.022
Bond angles : refined atoms 2108 2.378 1.964
Torsion angles, period 1. refined 190 6.194 5.000
Torsion angles, period 2. refined 74 28.982 23.784
Torsion angles, period 3. refined 216 13.563 15.000
Torsion angles, period 4. refined 10 16.921 15.000
Chiral centres: refined atoms 234 0.202 0.200
Planar groups: refined atoms 1212 0.013 0.020
VDW repulsions: refined atoms 627 0.220 0.200
VDW; torsion: refined atoms 1082 0.315 0.200
HBOND: refined atoms 134 0.150 0.200
VDW repulsions; symmetry: refined atoms 49 0.156 0.200
HBOND; symmetry: refined atoms 28 0.330 0.200
M. chain bond B values: refined atoms 969 1.760 1.500
M. chain angle B values: refined atoms 1558 2.701 2.000
S. chain bond B values: refined atoms 635 4.150 3.000
S. chain angle B values: refined atoms 550 6.413 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.852, B = 0.011
Partial structure 1: scale = 0.300, B = 19.949
Overall anisotropic scale factors
B11 = -0.57 B22 = 0.42 B33 = 0.15 B12 = 0.00 B13 = 0.00 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.008 243 100.00 356.8 358.2 0.19 0.23 10 333.2 322.8 0.19 0.23
0.023 384 100.00 279.2 292.0 0.17 0.21 21 271.9 301.3 0.20 0.27
0.038 477 100.00 312.0 313.6 0.13 0.17 28 305.4 323.2 0.14 0.20
0.052 544 96.62 343.8 338.9 0.11 0.15 27 405.4 397.6 0.10 0.13
0.067 612 98.32 314.7 305.2 0.13 0.15 33 302.3 280.4 0.14 0.17
0.082 676 99.58 300.2 285.2 0.13 0.16 41 287.0 262.1 0.19 0.23
0.097 737 99.87 254.4 241.6 0.15 0.16 38 275.2 253.1 0.16 0.19
0.112 771 99.64 208.9 201.3 0.15 0.16 53 212.3 195.2 0.20 0.21
0.127 831 99.77 180.4 175.4 0.17 0.18 44 207.1 191.1 0.18 0.21
0.142 868 99.78 163.4 159.9 0.17 0.17 47 148.0 150.6 0.22 0.24
0.156 940 99.60 152.5 149.1 0.16 0.17 51 135.0 136.7 0.17 0.18
0.171 934 99.20 133.5 131.4 0.17 0.17 60 127.3 122.6 0.25 0.25
0.186 995 99.15 126.0 123.9 0.16 0.16 55 122.8 124.3 0.22 0.22
0.201 1029 99.00 118.8 115.5 0.16 0.15 58 121.1 115.5 0.21 0.21
0.216 1043 98.30 113.7 110.2 0.16 0.15 55 95.2 97.9 0.23 0.22
0.231 1083 97.76 100.6 100.0 0.17 0.15 53 99.3 91.9 0.21 0.20
0.246 1132 97.54 95.9 94.7 0.15 0.14 59 102.2 105.4 0.22 0.21
0.260 1128 96.73 85.2 86.7 0.17 0.16 54 83.2 86.2 0.20 0.18
0.275 1144 93.70 73.1 75.7 0.18 0.15 61 71.5 78.6 0.25 0.21
0.290 758 61.35 58.6 69.2 0.30 0.23 34 53.6 72.0 0.44 0.29
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0078 131 0.939 112 0.832 243 0.889 1.019
0.0227 270 0.902 114 0.811 384 0.875 1.014
0.0375 359 0.916 118 0.856 477 0.901 1.009
0.0524 438 0.947 106 0.899 544 0.937 1.004
0.0673 500 0.946 112 0.851 612 0.928 0.999
0.0821 565 0.941 111 0.864 676 0.929 0.994
0.0970 623 0.926 114 0.868 737 0.917 0.989
0.1118 657 0.916 114 0.835 771 0.904 0.984
0.1267 717 0.900 114 0.837 831 0.891 0.979
0.1416 759 0.887 109 0.829 868 0.880 0.974
0.1564 823 0.888 117 0.837 940 0.882 0.969
0.1713 825 0.880 109 0.804 934 0.871 0.964
0.1861 882 0.881 113 0.789 995 0.871 0.959
0.2010 919 0.877 110 0.857 1029 0.875 0.954
0.2158 936 0.879 107 0.804 1043 0.872 0.950
0.2307 982 0.869 101 0.775 1083 0.860 0.945
0.2456 1021 0.877 111 0.818 1132 0.871 0.940
0.2604 1032 0.861 96 0.811 1128 0.857 0.935
0.2753 1046 0.843 98 0.775 1144 0.837 0.931
0.2901 719 0.822 39 0.847 758 0.823 0.926
$$
Resolution limits = 50.000 1.833
Number of used reflections = 16329
Percentage observed = 95.7230
Percentage of free reflections = 5.1246
Overall R factor = 0.1555
Free R factor = 0.1904
Overall weighted R factor = 0.1656
Free weighted R factor = 0.2075
Overall correlation coefficient = 0.9654
Free correlation coefficient = 0.9501
Cruickshanks DPI for coordinate error= 0.1259
DPI based on free R factor = 0.1171
Overall figure of merit = 0.8788
ML based su of positional parameters = 0.0754
ML based su of thermal parameters = 2.4975
-----------------------------------------------------------------------------
Time in seconds: CPU = 12.20
Elapsed = 0.00
**** 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:
$$
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$
$$
0 0.228 0.221 0.851 88700.2 0.028 4.533 0.163
1 0.184 0.201 0.872 85078.6 0.029 2.509 0.178
2 0.169 0.195 0.878 83708.6 0.030 2.448 0.194
3 0.162 0.193 0.879 83089.2 0.031 2.431 0.200
4 0.158 0.192 0.879 82787.4 0.031 2.404 0.202
5 0.155 0.190 0.879 82619.6 0.031 2.378 0.202
$$
Refmac_5.3.0040: End of Refmac_5.3.0040 Times: User: 14.7s System: 0.8s Elapsed: 0:16
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
CCP4i: Writing final coordinates (XYZOUT) to /home/pjx/PROJECTS/myProject/rnase_refmac4.pdb
CCP4i: Writing final phases (HKLOUT) to /home/pjx/PROJECTS/myProject/rnase18_refmac4.mtz
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