#CCP4I VERSION CCP4Interface 1.3.12
#CCP4I SCRIPT LOG refmac5
#CCP4I DATE 01 Aug 2003 11:06:50
#CCP4I USER mgwt
#CCP4I PROJECT 2003test
#CCP4I JOB_ID 161
#CCP4I SCRATCH /tmp/mgwt
#CCP4I HOSTNAME bunyip
#CCP4I PID 31438
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### CCP4 5.0: Refmac_5.1.9999 5.1.9999 ##########
###############################################################
User: mgwt Run date: 1/ 8/2003 Run time: 11:06:50
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--- 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=FNAT SIGFP=SIGFNAT 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
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /y/people/mgwt/CCP4/examples/tut2003/data/rnase18.mtz
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name - /y/people/mgwt/CCP4/examples/tut2003/data/rnase.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /y/people/mgwt/work/2003test_161_2_pdb_1.tmp
Input reflection file. Logical name - HKLIN actual file name - /y/people/mgwt/CCP4/examples/tut2003/data/rnase18.mtz
Output reflection file. Logical name - HKLOUT actual file name - /y/people/mgwt/work/2003test_161_4_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 - P212121
Refinement type : Restrained
**** Makecif parameters ****
Dictionary files for restraints : /y/programs/xtal/ccp4-5.0.c/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-5.0.c/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 0.0149
Refinement of individual isotropic Bfactors
Refinement resln : 50.0000 1.8330
Estimated number of reflections : 21795
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 1.8330
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 :/y/people/mgwt/CCP4/examples/tut2003/data/rnase.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.c/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 : 3567
Number of missing atoms : 1842
Number of rebuilt atoms : 1842
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 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 HE - A 40 ARG CZ mod.= 79.06 id.= 117.90 dev= 38.844 sig.= 3.000
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
A 72 CYS HB2 - A 72 CYS SG B mod.= 13.00 id.= 108.00 dev= 95.001 sig.= 3.000
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 HE - B 40 ARG CZ mod.= 85.09 id.= 117.90 dev= 32.805 sig.= 3.000
B 40 ARG CD - B 40 ARG CZ mod.= 157.00 id.= 124.20 dev=-32.795 sig.= 1.500
B 72 CYS HB1 - B 72 CYS SG B mod.= 18.72 id.= 108.00 dev= 89.279 sig.= 3.000
**** 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
w_average 0.417695791
GRID VALUES:
0.092105262 Angstrom for D
4.91666651 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.028 0.021
Bond distances: others 1298 0.000 0.020
Bond angles : refined atoms 2108 4.608 1.947
Bond angles : others 3022 4.822 3.000
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 0.167 0.200
Planar groups: refined atoms 1746 0.014 0.020
Planar groups: others 320 0.018 0.020
VDW repulsions: refined atoms 311 0.215 0.200
VDW repulsions: others 1227 0.255 0.200
VDW; torsion: refined atoms 763 0.194 0.200
VDW; torsion: others 736 0.135 0.200
HBOND: refined atoms 110 0.177 0.200
HBOND: others 1 0.043 0.200
VDW repulsions; symmetry: refined atoms 13 0.133 0.200
VDW repulsions; symmetry: others 53 0.304 0.200
HBOND; symmetry: refined atoms 26 0.399 0.200
M. chain bond B values: refined atoms 956 3.209 1.500
M. chain bond B values: others 392 0.000 1.500
M. chain angle B values: refined atoms 1558 4.517 2.000
M. chain angle B values: others 1296 3.419 2.000
S. chain bond B values: refined atoms 582 4.562 3.000
S. chain bond B values: others 906 0.000 3.000
S. chain angle B values: refined atoms 550 6.301 4.500
S. chain angle B values: others 1726 3.998 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.872, B = 2.461
Babinet"s bulk solvent: scale = 0.078, B = 293.900
Partial structure 1: scale = 0.346, B = 33.735
Overall anisotropic scale factors
B11 = -0.58 B22 = 0.47 B33 = 0.11 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle 1. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle 1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.008 243 100.00 348.8 329.1 0.19 0.23 10 325.6 336.8 0.15 0.21
0.023 384 100.00 272.9 272.2 0.17 0.22 21 265.8 277.4 0.20 0.27
0.038 477 100.00 305.0 306.1 0.17 0.23 28 298.5 318.0 0.13 0.18
0.052 544 96.62 336.0 337.0 0.17 0.22 27 396.3 412.6 0.13 0.16
0.067 612 98.32 307.5 299.5 0.19 0.23 33 295.5 263.7 0.20 0.25
0.082 676 99.58 293.4 274.9 0.19 0.22 41 280.5 242.9 0.21 0.23
0.097 737 99.87 248.6 234.0 0.21 0.23 38 268.9 247.7 0.18 0.22
0.112 771 99.64 204.2 195.2 0.22 0.24 53 207.5 194.1 0.26 0.26
0.127 831 99.77 176.3 168.9 0.24 0.25 44 202.4 178.1 0.25 0.28
0.142 868 99.78 159.7 155.1 0.25 0.25 47 144.7 141.4 0.26 0.25
0.156 940 99.60 149.1 144.1 0.24 0.25 51 132.0 126.8 0.27 0.26
0.171 934 99.20 130.5 125.8 0.24 0.24 60 124.4 124.5 0.22 0.22
0.186 995 99.15 123.2 118.3 0.26 0.25 55 120.0 114.6 0.24 0.25
0.201 1029 99.00 116.1 109.7 0.25 0.24 58 118.3 118.4 0.23 0.22
0.216 1043 98.30 111.2 103.2 0.26 0.25 55 93.0 92.3 0.31 0.30
0.231 1083 97.76 98.3 93.7 0.27 0.25 53 97.1 92.7 0.26 0.25
0.246 1132 97.54 93.8 88.4 0.27 0.25 59 99.9 97.7 0.22 0.23
0.260 1128 96.73 83.3 80.5 0.28 0.26 54 81.4 80.2 0.25 0.22
0.275 1144 93.70 71.5 71.3 0.29 0.26 61 69.9 66.1 0.33 0.28
0.290 758 61.35 57.3 66.2 0.41 0.33 34 52.4 62.8 0.47 0.37
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 1. Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
$GRAPHS:Cycle 1. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0078 131 0.919 112 0.802 243 0.865 0.903
0.0227 270 0.879 114 0.793 384 0.853 0.944
0.0375 359 0.909 118 0.832 477 0.890 0.971
0.0524 438 0.940 106 0.833 544 0.919 0.986
0.0673 500 0.932 112 0.849 612 0.917 0.994
0.0821 565 0.934 111 0.848 676 0.919 0.996
0.0970 623 0.902 114 0.850 737 0.894 0.994
0.1118 657 0.892 114 0.798 771 0.878 0.990
0.1267 717 0.878 114 0.780 831 0.865 0.984
0.1416 759 0.851 109 0.799 868 0.844 0.977
0.1564 823 0.855 117 0.813 940 0.850 0.969
0.1713 825 0.843 109 0.771 934 0.834 0.961
0.1861 882 0.843 113 0.712 995 0.828 0.952
0.2010 919 0.845 110 0.776 1029 0.838 0.943
0.2158 936 0.840 107 0.807 1043 0.836 0.935
0.2307 982 0.833 101 0.737 1083 0.824 0.926
0.2456 1021 0.838 111 0.784 1132 0.832 0.917
0.2604 1032 0.824 96 0.753 1128 0.818 0.908
0.2753 1046 0.805 98 0.734 1144 0.799 0.899
0.2901 719 0.779 39 0.821 758 0.782 0.891
$$
Resolution limits = 50.000 1.833
Number of used reflections = 16329
Percentage observed = 95.7230
Percentage of free reflections = 5.1246
Overall R factor = 0.2270
Free R factor = 0.2239
Overall weighted R factor = 0.2390
Free weighted R factor = 0.2381
Overall correlation coefficient = 0.9309
Free correlation coefficient = 0.9328
Cruickshanks DPI for coordinate error= 0.1838
DPI based on free R factor = 0.1377
Overall figure of merit = 0.8472
ML based su of positional parameters = 0.0980
ML based su of thermal parameters = 3.3006
-----------------------------------------------------------------------------
Trying gamma equal 0.
Trying gamma equal 0.0500000007
Gamma decreased to 0.0399999991
CGMAT cycle number = 2
w_average 0.430792034
GRID VALUES:
0.092105262 Angstrom for D
4.92000008 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.025 0.021
Bond distances: others 1298 0.009 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.870, B = -0.268
Babinet"s bulk solvent: scale = 0.077, B = 293.902
Partial structure 1: scale = 0.347, B = 34.574
Overall anisotropic scale factors
B11 = -0.58 B22 = 0.47 B33 = 0.11 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1839
Free R factor = 0.2027
Overall figure of merit = 0.8719
-----------------------------------------------------------------------------
Trying gamma equal 0.0399999991
Gamma decreased to 0.0309090894
CGMAT cycle number = 3
w_average 0.435811967
GRID VALUES:
0.092105262 Angstrom for D
5.01923084 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.023 0.021
Bond distances: others 1298 0.005 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.867, B = -0.103
Babinet"s bulk solvent: scale = 0.068, B = 293.896
Partial structure 1: scale = 0.349, B = 32.676
Overall anisotropic scale factors
B11 = -0.58 B22 = 0.47 B33 = 0.11 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1700
Free R factor = 0.1931
Overall figure of merit = 0.8815
-----------------------------------------------------------------------------
Trying gamma equal 0.0309090894
Gamma decreased to 0.022644626
CGMAT cycle number = 4
w_average 0.43794772
GRID VALUES:
0.092105262 Angstrom for D
4.96428585 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.022 0.021
Bond distances: others 1298 0.001 0.020
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.868, B = -0.015
Babinet"s bulk solvent: scale = 0.067, B = 293.895
Partial structure 1: scale = 0.350, B = 32.523
Overall anisotropic scale factors
B11 = -0.58 B22 = 0.47 B33 = 0.11 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.1627
Free R factor = 0.1883
Overall figure of merit = 0.8855
-----------------------------------------------------------------------------
Trying gamma equal 0.022644626
Gamma decreased to 0.0151314782
CGMAT cycle number = 5
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 72 CYS HB2 - A 72 CYS SG B mod.= 59.41 id.= 108.00 dev= 48.587 sig.= 3.000
A 72 CYS CA - A 72 CYS HB2 mod.= 68.52 id.= 109.00 dev= 40.477 sig.= 3.000
B 72 CYS HB1 - B 72 CYS SG B mod.= 60.56 id.= 108.00 dev= 47.440 sig.= 3.000
w_average 0.438797057
GRID VALUES:
0.092105262 Angstrom for D
4.91666651 Angstrom^2 for B
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.021 0.021
Bond distances: others 1298 0.001 0.020
Bond angles : refined atoms 2108 1.903 1.947
Bond angles : others 3022 1.962 3.000
Torsion angles, period 1. refined 190 5.993 5.000
Torsion angles, period 2. refined 74 29.030 23.784
Torsion angles, period 3. refined 216 13.801 15.000
Torsion angles, period 4. refined 10 19.753 15.000
Chiral centres: refined atoms 234 0.120 0.200
Planar groups: refined atoms 1746 0.008 0.020
Planar groups: others 320 0.001 0.020
VDW repulsions: refined atoms 297 0.212 0.200
VDW repulsions: others 1282 0.196 0.200
VDW; torsion: refined atoms 795 0.190 0.200
VDW; torsion: others 885 0.096 0.200
HBOND: refined atoms 124 0.155 0.200
VDW repulsions; symmetry: refined atoms 9 0.066 0.200
VDW repulsions; symmetry: others 44 0.308 0.200
HBOND; symmetry: refined atoms 25 0.341 0.200
M. chain bond B values: refined atoms 1184 1.676 1.500
M. chain bond B values: others 392 0.346 1.500
M. chain angle B values: refined atoms 1558 2.121 2.000
M. chain angle B values: others 1296 0.943 2.000
S. chain bond B values: refined atoms 679 3.301 3.000
S. chain bond B values: others 1120 1.174 3.000
S. chain angle B values: refined atoms 550 4.926 4.500
S. chain angle B values: others 1726 2.156 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.867, B = 0.030
Babinet"s bulk solvent: scale = 0.069, B = 293.893
Partial structure 1: scale = 0.349, B = 31.799
Overall anisotropic scale factors
B11 = -0.58 B22 = 0.47 B33 = 0.11 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle 5. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle 5. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.008 243 100.00 350.7 333.3 0.18 0.21 10 327.4 335.0 0.18 0.23
0.023 384 100.00 274.4 281.9 0.15 0.20 21 267.3 283.2 0.14 0.20
0.038 477 100.00 306.7 314.7 0.14 0.18 28 300.2 325.4 0.13 0.17
0.052 544 96.62 337.9 339.1 0.12 0.16 27 398.4 409.3 0.11 0.14
0.067 612 98.32 309.2 301.9 0.14 0.16 33 297.1 274.9 0.14 0.17
0.082 676 99.58 295.1 279.3 0.14 0.16 41 282.0 260.5 0.19 0.24
0.097 737 99.87 250.0 236.2 0.15 0.17 38 270.4 245.2 0.17 0.21
0.112 771 99.64 205.3 197.8 0.15 0.16 53 208.6 198.1 0.22 0.23
0.127 831 99.77 177.3 172.2 0.17 0.18 44 203.5 186.1 0.19 0.21
0.142 868 99.78 160.5 157.4 0.17 0.17 47 145.5 144.4 0.22 0.24
0.156 940 99.60 149.9 146.0 0.17 0.17 51 132.7 133.5 0.17 0.18
0.171 934 99.20 131.2 128.5 0.17 0.17 60 125.1 123.4 0.22 0.22
0.186 995 99.15 123.8 121.4 0.17 0.16 55 120.7 119.1 0.24 0.24
0.201 1029 99.00 116.7 113.1 0.16 0.16 58 119.0 115.4 0.22 0.22
0.216 1043 98.30 111.8 108.2 0.16 0.15 55 93.6 92.7 0.23 0.21
0.231 1083 97.76 98.9 97.6 0.17 0.16 53 97.6 94.9 0.19 0.18
0.246 1132 97.54 94.3 92.9 0.16 0.14 59 100.5 101.8 0.20 0.19
0.260 1128 96.73 83.8 84.3 0.17 0.16 54 81.8 83.4 0.18 0.16
0.275 1144 93.70 71.9 73.6 0.18 0.15 61 70.3 73.2 0.23 0.19
0.290 758 61.35 57.6 66.9 0.29 0.22 34 52.7 68.3 0.42 0.29
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 5. Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
$GRAPHS:Cycle 5. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0078 131 0.932 112 0.826 243 0.883 0.890
0.0227 270 0.900 114 0.810 384 0.873 0.938
0.0375 359 0.919 118 0.848 477 0.901 0.970
0.0524 438 0.950 106 0.895 544 0.939 0.989
0.0673 500 0.948 112 0.859 612 0.932 1.000
0.0821 565 0.946 111 0.870 676 0.934 1.004
0.0970 623 0.929 114 0.871 737 0.920 1.004
0.1118 657 0.923 114 0.838 771 0.910 1.001
0.1267 717 0.908 114 0.850 831 0.900 0.997
0.1416 759 0.892 109 0.838 868 0.885 0.991
0.1564 823 0.895 117 0.847 940 0.889 0.984
0.1713 825 0.886 109 0.813 934 0.878 0.976
0.1861 882 0.888 113 0.789 995 0.877 0.969
0.2010 919 0.887 110 0.856 1029 0.884 0.961
0.2158 936 0.889 107 0.822 1043 0.882 0.953
0.2307 982 0.878 101 0.792 1083 0.870 0.945
0.2456 1021 0.889 111 0.832 1132 0.884 0.936
0.2604 1032 0.872 96 0.831 1128 0.869 0.928
0.2753 1046 0.858 98 0.792 1144 0.852 0.920
0.2901 719 0.840 39 0.877 758 0.841 0.913
$$
Resolution limits = 50.000 1.833
Number of used reflections = 16329
Percentage observed = 95.7230
Percentage of free reflections = 5.1246
Overall R factor = 0.1584
Free R factor = 0.1870
Overall weighted R factor = 0.1690
Free weighted R factor = 0.2048
Overall correlation coefficient = 0.9639
Free correlation coefficient = 0.9534
Cruickshanks DPI for coordinate error= 0.1283
DPI based on free R factor = 0.1151
Overall figure of merit = 0.8869
ML based su of positional parameters = 0.0740
ML based su of thermal parameters = 2.4609
-----------------------------------------------------------------------------
Trying gamma equal 0.0151314782
Gamma decreased to 0.00830134377
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 72 CYS HB2 - A 72 CYS SG B mod.= 59.62 id.= 108.00 dev= 48.384 sig.= 3.000
A 72 CYS CA - A 72 CYS HB2 mod.= 67.98 id.= 109.00 dev= 41.019 sig.= 3.000
B 72 CYS HB1 - B 72 CYS SG B mod.= 61.11 id.= 108.00 dev= 46.894 sig.= 3.000
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /y/people/mgwt/work/2003test_161_4_mtz_1.tmp
* Title:
Output mtz file from refmac
* Base dataset:
0 HKL_base
HKL_base
HKL_base
* Number of Datasets = 1
* Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:
1 RNASE
RNASE
NATIVE
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
0.00000
* Number of Columns = 13
* Number of Reflections = 17948
* Missing value set to NaN in input mtz file
* HISTORY for current MTZ file :
* Column Labels, Types, Ranges [and Dataset IDs] :
H H 0.0000 35.0000 0
K H 0.0000 42.0000 0
L H 0.0000 21.0000 0
FNAT F 2.1871 1405.2971 1
SIGFNAT Q 1.0932 83.0021 1
FreeR_flag I 0.0000 19.0000 1
FC F 0.0330 7610.6685 1
PHIC P 0.0000 360.0000 1
FWT F 0.0008 1800.6226 1
PHWT P 0.0000 360.0000 1
DELFWT F 0.0000 395.3254 1
PHDELWT P 0.0000 360.0000 1
FOM W 0.0000 1.0000 1
* Cell Dimensions : (obsolete - use crystal cells)
64.8970 78.3230 38.7920 90.0000 90.0000 90.0000
* Resolution Range :
0.00040 0.29717 ( 49.972 - 1.834 A )
* Sort Order :
1 2 3 0 0
* Number of Symmetry Operations = 4
* Number of Primitive Operations = 4
* Space Group = 19 P212121
* Lattice Type = P
* Point Group Name = PG222
* 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+1/2, -Y, Z+1/2
-1.00 0.00 0.00 0.50
0.00 -1.00 0.00 0.00
0.00 0.00 1.00 0.50
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, Y+1/2, -Z+1/2
-1.00 0.00 0.00 0.00
0.00 1.00 0.00 0.50
0.00 0.00 -1.00 0.50
0.00 0.00 0.00 1.00
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1538 0.021 0.021
Bond distances: others 1298 0.002 0.020
Bond angles : refined atoms 2108 1.853 1.947
Bond angles : others 3022 1.951 3.000
Torsion angles, period 1. refined 190 6.017 5.000
Torsion angles, period 2. refined 74 28.949 23.784
Torsion angles, period 3. refined 216 13.935 15.000
Torsion angles, period 4. refined 10 19.173 15.000
Chiral centres: refined atoms 234 0.118 0.200
Planar groups: refined atoms 1746 0.008 0.020
Planar groups: others 320 0.001 0.020
VDW repulsions: refined atoms 293 0.213 0.200
VDW repulsions: others 1297 0.193 0.200
VDW; torsion: refined atoms 796 0.190 0.200
VDW; torsion: others 898 0.095 0.200
HBOND: refined atoms 125 0.150 0.200
VDW repulsions; symmetry: refined atoms 7 0.074 0.200
VDW repulsions; symmetry: others 48 0.295 0.200
HBOND; symmetry: refined atoms 26 0.326 0.200
M. chain bond B values: refined atoms 1184 1.637 1.500
M. chain bond B values: others 392 0.339 1.500
M. chain angle B values: refined atoms 1558 2.079 2.000
M. chain angle B values: others 1296 0.926 2.000
S. chain bond B values: refined atoms 678 3.238 3.000
S. chain bond B values: others 1128 1.146 3.000
S. chain angle B values: refined atoms 550 4.924 4.500
S. chain angle B values: others 1726 2.150 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.868, B = 0.069
Babinet"s bulk solvent: scale = 0.067, B = 293.892
Partial structure 1: scale = 0.350, B = 31.136
Overall anisotropic scale factors
B11 = -0.58 B22 = 0.47 B33 = 0.11 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle 6. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle 6. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.008 243 100.00 350.6 333.5 0.18 0.21 10 327.3 333.1 0.18 0.23
0.023 384 100.00 274.3 282.9 0.15 0.20 21 267.2 284.2 0.14 0.21
0.038 477 100.00 306.5 315.0 0.14 0.18 28 300.1 324.9 0.13 0.17
0.052 544 96.62 337.8 338.6 0.12 0.15 27 398.3 408.9 0.11 0.14
0.067 612 98.32 309.1 301.4 0.13 0.16 33 297.0 277.3 0.14 0.17
0.082 676 99.58 294.9 279.3 0.14 0.16 41 281.9 261.2 0.20 0.24
0.097 737 99.87 249.9 236.3 0.15 0.17 38 270.3 244.6 0.17 0.21
0.112 771 99.64 205.2 197.7 0.15 0.16 53 208.6 197.9 0.22 0.23
0.127 831 99.77 177.2 172.5 0.17 0.18 44 203.4 187.1 0.18 0.21
0.142 868 99.78 160.5 157.4 0.17 0.17 47 145.4 144.8 0.23 0.24
0.156 940 99.60 149.8 146.1 0.16 0.17 51 132.7 134.0 0.17 0.17
0.171 934 99.20 131.1 128.6 0.17 0.17 60 125.0 122.6 0.22 0.22
0.186 995 99.15 123.8 121.4 0.16 0.16 55 120.6 119.4 0.24 0.25
0.201 1029 99.00 116.7 113.2 0.16 0.15 58 118.9 114.6 0.23 0.22
0.216 1043 98.30 111.7 108.3 0.16 0.15 55 93.5 92.8 0.22 0.21
0.231 1083 97.76 98.8 97.7 0.17 0.15 53 97.6 94.8 0.20 0.19
0.246 1132 97.54 94.2 93.1 0.15 0.14 59 100.4 101.6 0.19 0.18
0.260 1128 96.73 83.7 84.3 0.17 0.15 54 81.8 83.4 0.18 0.17
0.275 1144 93.70 71.8 73.6 0.17 0.15 61 70.3 73.6 0.22 0.19
0.290 758 61.35 57.6 66.8 0.29 0.22 34 52.7 69.0 0.44 0.30
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 6. Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
$GRAPHS:Cycle 6. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0078 131 0.932 112 0.825 243 0.883 0.890
0.0227 270 0.900 114 0.811 384 0.874 0.939
0.0375 359 0.919 118 0.850 477 0.902 0.971
0.0524 448 0.950 116 0.906 564 0.941 0.990
0.0673 505 0.948 117 0.859 622 0.932 1.001
0.0821 566 0.947 113 0.874 679 0.935 1.005
0.0970 623 0.931 115 0.873 738 0.922 1.006
0.1118 659 0.923 115 0.837 774 0.910 1.003
0.1267 717 0.909 116 0.853 833 0.901 0.999
0.1416 760 0.894 110 0.842 870 0.887 0.993
0.1564 823 0.896 120 0.857 943 0.891 0.986
0.1713 826 0.887 116 0.816 942 0.879 0.979
0.1861 887 0.890 117 0.792 1004 0.878 0.972
0.2010 924 0.887 116 0.850 1040 0.883 0.964
0.2158 945 0.889 117 0.814 1062 0.881 0.956
0.2307 996 0.880 110 0.789 1106 0.871 0.948
0.2456 1040 0.886 122 0.829 1162 0.880 0.940
0.2604 1051 0.873 114 0.837 1165 0.869 0.932
0.2753 1100 0.859 120 0.802 1220 0.853 0.924
0.2901 1095 0.846 111 0.850 1206 0.846 0.916
$$
Resolution limits = 50.000 1.833
Number of used reflections = 16329
Percentage observed = 95.7230
Percentage of free reflections = 5.1246
Overall R factor = 0.1556
Free R factor = 0.1872
Overall weighted R factor = 0.1661
Free weighted R factor = 0.2050
Overall correlation coefficient = 0.9651
Free correlation coefficient = 0.9539
Cruickshanks DPI for coordinate error= 0.1260
DPI based on free R factor = 0.1152
Overall figure of merit = 0.8862
ML based su of positional parameters = 0.0740
ML based su of thermal parameters = 2.4609
-----------------------------------------------------------------------------
Time in seconds: CPU = 31.69
Elapsed = 68.00
**** Things for loggraph, R factor and others vs cycle ****
$TABLE: Rfactor analysis, stats vs cycle :
$GRAPHS:<Rfactor> 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:
$$
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$
$$
0 0.227 0.224 0.847 87940.6 0.028 4.608 0.167
1 0.184 0.203 0.872 84528.8 0.025 2.504 0.140
2 0.170 0.193 0.882 83263.4 0.023 2.144 0.130
3 0.163 0.188 0.885 82572.6 0.022 1.989 0.123
4 0.158 0.187 0.887 82210.4 0.021 1.903 0.120
5 0.156 0.187 0.886 85263.9 0.021 1.853 0.118
$$
Harvest: NO PNAME_KEYWRD given - no deposit file created
Refmac_5.1.9999: End of Refmac_5.1.9999
Times: User: 39.8s System: 1.9s Elapsed: 1:39
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Writing final coordinates to /y/people/mgwt/TEST/rnase_refmac2.pdb
***************************************************************************
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
Writing final phases to /y/people/mgwt/TEST/rnase18_refmac2.mtz
***************************************************************************
#CCP4I TERMINATION STATUS 1
#CCP4I TERMINATION TIME 01 Aug 2003 11:08:29
#CCP4I MESSAGE Task completed successfully