The logfile is composed of output from the following programs:
Result:
165 residues were built in 3 chains, the longest having 73 residues. 125 residues were sequenced, after pruning.
Current view: summary only [Show full logfile] [Hide logfile]
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############################################################### ############################################################### ############################################################### ### CCP4 6.0: cbuccaneer version 1.0.0 : 04/10/07## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:08:08 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.
Copyright 2002-2007 Kevin Cowtan and University of York.
$TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$
title [No title given] pdbin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.mtz colin-ref-fo /*/*/[FP.F_sigF.F,FP.F_sigF.sigF] colin-ref-hl /*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D] seqin-wrk /home/cowtan/test/1vjf.seq mtzin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz colin-wrk-fo /*/*/[FP,SIGFP] colin-wrk-free /*/*/[FreeR_flag] colin-wrk-hl /*/*/[pirate.ABCD.A,pirate.ABCD.B,pirate.ABCD.C,pirate.ABCD.D] pdbout-wrk /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb find grow join link sequence correct filter ncsbuild prune rebuild cycles 3 sequence-reliability 0.95 new-residue-name UNK resolution 2.0 Cycle: 1 C-alphas after finding: 24 C-alphas after growing: 337 C-alphas after joining: 211 C-alphas linked: 0 C-alphas sequenced: 115 C-alphas corrected: 0 C-alphas after filtering: 211 C-alphas after NCS build: 211 C-alphas after pruning: 146 C-alphas after rebuilding: 146
Internal cycle 1 146 residues were built in 6 chains, the longest having 33 residues. 108 residues were sequenced, after pruning.
Cycle: 2 C-alphas after finding: 170 C-alphas after growing: 421 C-alphas after joining: 218 C-alphas linked: 0 C-alphas sequenced: 146 C-alphas corrected: 0 C-alphas after filtering: 196 C-alphas after NCS build: 196 C-alphas after pruning: 170 C-alphas after rebuilding: 170
Internal cycle 2 170 residues were built in 5 chains, the longest having 73 residues. 128 residues were sequenced, after pruning.
Cycle: 3 C-alphas after finding: 194 C-alphas after growing: 311 C-alphas after joining: 211 C-alphas linked: 1 C-alphas sequenced: 133 C-alphas corrected: 0 C-alphas after filtering: 199 C-alphas after NCS build: 199 C-alphas after pruning: 165 C-alphas after rebuilding: 165
Internal cycle 3 165 residues were built in 3 chains, the longest having 73 residues. 125 residues were sequenced, after pruning.
$TEXT:Result: $$ $$ 165 residues were built in 3 chains, the longest having 73 residues. 125 residues were sequenced, after pruning. $$
cbuccaneer: Normal termination Times: User: 197.1s System: 0.4s Elapsed: 3:19
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
| Initial | After 10 cycles | |
|---|---|---|
| R factor | 0.443 | 0.326 |
| Rfree | 0.500 | 0.458 |
|
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 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. 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 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. 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_5.3.0037 version 5.3.0037 : 03/29/06## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:11:28 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--- title [No title given]
TITL
Data line--- weight MATRIX 0.1
WEIG
Data line--- labin HLA=pirate.ABCD.A HLB=pirate.ABCD.B HLC=pirate.ABCD.C HLD=pirate.ABCD.D FREE=FreeR_flag FP=FP SIGFP=SIGFP
LABI
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 PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT
REFI
Data line--- ncyc 10
NCYC
Data line--- scal type SIMP LSSC ANISO EXPE
SCAL
Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
SOLV
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--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
LABO
Data line--- PNAME buccaneer
PNAM
Data line--- DNAME buccaneer
DNAM
Data line--- RSIZE 80
RSIZ
Data line--- END
END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /home/cowtan/test/1vjf-3.2A.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name - /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
Input reflection file. Logical name - HKLIN actual file name - /home/cowtan/test/1vjf-3.2A.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
Cell from mtz : 50.903 50.903 121.411 90.000 90.000 90.000
Space group from mtz: number - 96; name - P43212
Refinement type : Restrained
**** Makecif parameters ****
Dictionary files for restraints : /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/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 : Phase modified Maximum Likelihood for Fs
Phase Blurred by Scale*Exp(-B s**2) : 1.00 0.00
**** 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 1.400
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 0.0049
Refinement of individual isotropic Bfactors
Refinement resln : 46.9323 3.2002
Estimated number of reflections : 3404
Free R exclusion - flag equals: 0
Weighting by comparison of trace of matrix
Weighting parameters : 0.1000
Refinement cycles : 10
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
Input phases not used in SigmaA estimation
Scaling and SigmaA resln: 46.9323 3.2002
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/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.12
_lib_update 20/09/07
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2436
with complete description : 454
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: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/atomsf.lib
Number of atoms : 1138
Number of residues : 165
Number of chains : 3
I am reading library. Please wait.
mon_lib.cif
INFO: link is found (not be used) dist= 1.389 ideal_dist= 1.500
ch:AA res: 137 ASP at:CG .->ch:BB res: 98 UNK at:CB .
INFO: link is found (not be used) dist= 1.386 ideal_dist= 1.337
ch:AA res: 137 ASP at:OD1 .->ch:BB res: 98 UNK at:CB .
INFO: link is found (not be used) dist= 1.364 ideal_dist= 1.337
ch:AA res: 137 ASP at:OD2 .->ch:BB res: 98 UNK at:CB .
INFO: link is found (not be used) dist= 1.510 ideal_dist= 1.410
ch:BB res: 65 LYS at:NZ .->ch:BB res: 92 ARG at:NH1 .
INFO: link is found (not be used) dist= 1.444 ideal_dist= 1.530
ch:CC res: 13 UNK at:CB .->ch:CC res: 18 UNK at:CB .
--------------------------------
--- title of input coord file ---
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-XX
--------------------------------
ATTENTION: atom:CB UNK 116 AA is missing in the structure
ATTENTION: atom:CB UNK 123 AA is missing in the structure
ATTENTION: atom:O VAL 179 AA is missing in the structure
ATTENTION: atom:CB UNK 63 BB is missing in the structure
ATTENTION: atom:O UNK 100 BB is missing in the structure
ATTENTION: atom:O UNK 26 CC is missing in the structure
Number of chains : 3
Total number of monomers : 165
Number of atoms : 1144
Number of missing atoms : 6
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0
Number of bonds restraints : 1154
Number of angles restraints : 1568
Number of torsions restraints : 769
Number of chiralities : 191
Number of planar groups : 205
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 2948
Number of reflection read 2948
CGMAT cycle number = 1
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 107 UNK CA . - A 107 UNK C . mod.= 1.273 id.= 1.525 dev= 0.252 sig.= 0.021
A 108 UNK C . - A 109 UNK N . mod.= 1.082 id.= 1.329 dev= 0.247 sig.= 0.014
A 119 ILE C . - A 120 ASN N . mod.= 1.098 id.= 1.329 dev= 0.231 sig.= 0.014
A 143 PRO CD . - A 143 PRO N . mod.= 2.054 id.= 1.473 dev= -0.581 sig.= 0.014
A 143 PRO C . - A 144 LEU N . mod.= 1.157 id.= 1.329 dev= 0.172 sig.= 0.014
A 164 LEU C . - A 165 GLY N . mod.= 1.065 id.= 1.329 dev= 0.264 sig.= 0.014
A 168 PRO CD . - A 168 PRO N . mod.= 2.067 id.= 1.473 dev= -0.594 sig.= 0.014
B 36 UNK C . - B 37 UNK N . mod.= 1.077 id.= 1.329 dev= 0.252 sig.= 0.014
B 38 UNK C . - B 39 VAL N . mod.= 1.063 id.= 1.329 dev= 0.266 sig.= 0.014
B 53 PRO CD . - B 53 PRO N . mod.= 2.070 id.= 1.473 dev= -0.597 sig.= 0.014
B 56 HIS C . - B 57 THR N . mod.= 1.135 id.= 1.329 dev= 0.194 sig.= 0.014
B 58 LYS C . - B 59 ASN N . mod.= 0.920 id.= 1.329 dev= 0.409 sig.= 0.014
B 65 LYS C . - B 66 GLY N . mod.= 1.115 id.= 1.329 dev= 0.214 sig.= 0.014
B 74 LEU C . - B 75 GLY N . mod.= 0.684 id.= 1.329 dev= 0.645 sig.= 0.014
B 75 GLY C . - B 76 GLU N . mod.= 1.066 id.= 1.329 dev= 0.263 sig.= 0.014
B 86 HIS C . - B 87 VAL N . mod.= 1.089 id.= 1.329 dev= 0.240 sig.= 0.014
B 89 GLY C . - B 90 SER N . mod.= 1.137 id.= 1.329 dev= 0.192 sig.= 0.014
B 91 GLY N . - B 91 GLY CA . mod.= 1.200 id.= 1.458 dev= 0.258 sig.= 0.021
C 18 UNK C . - C 19 UNK N . mod.= 1.187 id.= 1.329 dev= 0.142 sig.= 0.014
C 19 UNK N . - C 19 UNK CA . mod.= 1.144 id.= 1.458 dev= 0.314 sig.= 0.021
C 19 UNK C . - C 20 UNK N . mod.= 1.117 id.= 1.329 dev= 0.212 sig.= 0.014
C 23 UNK C . - C 24 UNK N . mod.= 0.967 id.= 1.329 dev= 0.362 sig.= 0.014
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 110 UNK O - A 111 PRO N mod.= 95.24 id.= 123.00 dev= 27.757 sig.= 1.600
A 110 UNK CA - A 111 PRO N mod.= 143.93 id.= 116.90 dev=-27.030 sig.= 1.500
A 110 UNK C - A 111 PRO CD mod.= 57.78 id.= 125.00 dev= 67.217 sig.= 4.100
A 137 ASP C - A 138 PRO CD mod.= 82.23 id.= 125.00 dev= 42.771 sig.= 4.100
A 143 PRO CA - A 143 PRO CD mod.= 87.18 id.= 112.00 dev= 24.816 sig.= 1.400
A 143 PRO N - A 143 PRO CG mod.= 80.17 id.= 103.20 dev= 23.033 sig.= 1.500
A 144 LEU C - A 145 LYS CA mod.= 140.79 id.= 121.70 dev=-19.093 sig.= 1.800
A 164 LEU O - A 165 GLY N mod.= 100.92 id.= 123.00 dev= 22.076 sig.= 1.600
A 164 LEU CA - A 165 GLY N mod.= 138.22 id.= 116.20 dev=-22.020 sig.= 2.000
A 164 LEU C - A 165 GLY CA mod.= 148.71 id.= 121.70 dev=-27.006 sig.= 1.800
A 168 PRO CA - A 168 PRO CD mod.= 85.51 id.= 112.00 dev= 26.489 sig.= 1.400
A 168 PRO N - A 168 PRO CG mod.= 80.58 id.= 103.20 dev= 22.618 sig.= 1.500
B 53 PRO CA - B 53 PRO CD mod.= 85.32 id.= 112.00 dev= 26.676 sig.= 1.400
B 53 PRO N - B 53 PRO CG mod.= 80.58 id.= 103.20 dev= 22.625 sig.= 1.500
B 58 LYS O - B 59 ASN N mod.= 93.56 id.= 123.00 dev= 29.442 sig.= 1.600
B 58 LYS CA - B 59 ASN N mod.= 145.52 id.= 116.20 dev=-29.320 sig.= 2.000
B 58 LYS C - B 59 ASN CA mod.= 148.69 id.= 121.70 dev=-26.988 sig.= 1.800
B 74 LEU O - B 75 GLY N mod.= 100.90 id.= 123.00 dev= 22.099 sig.= 1.600
B 74 LEU CA - B 75 GLY N mod.= 138.20 id.= 116.20 dev=-22.001 sig.= 2.000
B 74 LEU C - B 75 GLY CA mod.= 151.95 id.= 121.70 dev=-30.253 sig.= 1.800
B 90 SER C - B 91 GLY CA mod.= 154.09 id.= 121.70 dev=-32.390 sig.= 1.800
B 91 GLY N - B 91 GLY C mod.= 147.32 id.= 112.50 dev=-34.817 sig.= 2.900
C 19 UNK N - C 19 UNK C mod.= 141.21 id.= 111.20 dev=-30.009 sig.= 2.800
C 19 UNK O - C 20 UNK N mod.= 106.68 id.= 123.00 dev= 16.315 sig.= 1.600
**** Large deviation of atoms from planarity ****
Deviations from the planarity >10.000Sigma will be monitored
Atom: A 111 PRO N deviation= 0.25 sigma.= 0.02
Atom: A 138 PRO N deviation= -0.35 sigma.= 0.02
Atom: A 143 PRO N deviation= -0.29 sigma.= 0.02
Atom: A 168 PRO N deviation= 0.33 sigma.= 0.02
Atom: B 52 MET C deviation= 0.21 sigma.= 0.02
Atom: B 53 PRO N deviation= -0.42 sigma.= 0.02
**** VDW outliers ****
VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored
A 122 THR CB . - B 65 LYS NZ . mod.= 1.140 id.= 3.550 dev= -2.41 sig.= 0.20 sym.= 4 0 -1 0
A 122 THR CB . - B 65 LYS CE . mod.= 1.632 id.= 3.870 dev= -2.24 sig.= 0.20 sym.= 4 0 -1 0
A 122 THR CG2 . - B 65 LYS NZ . mod.= 1.286 id.= 3.540 dev= -2.25 sig.= 0.20 sym.= 4 0 -1 0
A 137 ASP CG . - B 98 UNK CB . mod.= 1.389 id.= 3.690 dev= -2.30 sig.= 0.20 sym.= 1 0 0 0
A 137 ASP OD1 . - B 98 UNK CB . mod.= 1.386 id.= 3.460 dev= -2.07 sig.= 0.20 sym.= 1 0 0 0
A 137 ASP OD2 . - B 98 UNK CB . mod.= 1.364 id.= 3.460 dev= -2.10 sig.= 0.20 sym.= 1 0 0 0
C 13 UNK CB . - C 18 UNK CB . mod.= 1.444 id.= 3.880 dev= -2.44 sig.= 0.20 sym.= 1 0 0 0
weigth matrix 0.1000000
special position ----------- 3.338314
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.055 0.022
Bond angles : refined atoms 1568 4.884 1.952
Torsion angles, period 1. refined 162 4.652 5.000
Torsion angles, period 2. refined 37 40.119 23.514
Torsion angles, period 3. refined 163 6.804 15.000
Torsion angles, period 4. refined 6 8.389 15.000
Chiral centres: refined atoms 191 0.179 0.200
Planar groups: refined atoms 861 0.031 0.020
VDW repulsions: refined atoms 668 0.563 0.200
VDW; torsion: refined atoms 815 0.350 0.200
HBOND: refined atoms 48 0.248 0.200
VDW repulsions; symmetry: refined atoms 89 0.703 0.200
HBOND; symmetry: refined atoms 4 0.364 0.200
M. chain bond B values: refined atoms 810 0.000 1.500
M. chain angle B values: refined atoms 1256 0.000 2.000
S. chain bond B values: refined atoms 344 0.000 3.000
S. chain angle B values: refined atoms 312 0.000 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.518, B = -41.796
Partial structure 1: scale = 0.289, B = 1.832
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.003 46 96.23 516.0 431.4 0.43 0.49 5 601.5 556.7 0.62 0.71
0.008 70 98.63 768.0 621.3 0.38 0.44 2 450.6 291.3 0.35 0.38
0.013 80 100.00 698.3 604.0 0.39 0.39 9 593.0 462.6 0.35 0.37
0.017 93 100.00 497.0 525.5 0.44 0.42 6 534.3 360.5 0.61 0.64
0.022 102 100.00 479.9 535.6 0.44 0.45 4 658.6 580.2 0.44 0.39
0.027 129 100.00 499.1 499.1 0.43 0.43 2 771.5 358.8 0.60 0.58
0.032 112 98.41 494.6 472.2 0.46 0.45 12 559.9 415.0 0.48 0.43
0.037 125 100.00 633.2 565.5 0.43 0.43 9 674.1 479.8 0.47 0.39
0.042 141 100.00 699.4 613.7 0.44 0.44 5 803.5 334.9 0.58 0.57
0.047 148 100.00 678.1 600.1 0.41 0.42 3 618.1 489.3 0.77 0.74
0.051 159 100.00 680.3 598.2 0.40 0.41 6 823.6 566.0 0.51 0.49
0.056 159 100.00 768.1 591.9 0.40 0.39 4 602.3 555.9 0.48 0.47
0.061 158 100.00 686.6 551.0 0.44 0.43 9 679.9 289.6 0.66 0.58
0.066 167 100.00 608.9 518.6 0.47 0.46 6 664.6 554.7 0.43 0.49
0.071 181 100.00 628.0 522.2 0.46 0.44 5 820.1 702.5 0.30 0.33
0.076 180 100.00 636.7 570.9 0.48 0.45 11 650.4 455.0 0.37 0.35
0.081 178 100.00 611.6 508.9 0.42 0.43 14 487.6 457.2 0.64 0.53
0.085 185 100.00 549.9 498.8 0.54 0.50 8 439.0 457.9 0.64 0.46
0.090 194 100.00 516.8 465.5 0.48 0.47 11 688.3 512.9 0.39 0.38
0.095 192 100.00 542.7 456.1 0.47 0.46 12 393.7 432.5 0.53 0.48
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0029 13 0.980 33 0.901 46 0.923 0.821
0.0077 30 0.944 40 0.956 70 0.951 0.824
0.0126 41 0.917 39 0.875 80 0.897 0.827
0.0175 56 0.936 37 0.819 93 0.889 0.829
0.0223 64 0.919 38 0.852 102 0.894 0.831
0.0272 81 0.922 48 0.816 129 0.882 0.833
0.0320 73 0.919 39 0.845 112 0.893 0.834
0.0369 86 0.915 39 0.814 125 0.883 0.836
0.0418 100 0.945 41 0.842 141 0.915 0.837
0.0466 109 0.920 39 0.840 148 0.899 0.839
0.0515 113 0.917 46 0.825 159 0.891 0.840
0.0563 114 0.932 45 0.874 159 0.916 0.841
0.0612 122 0.928 36 0.811 158 0.902 0.842
0.0661 124 0.886 43 0.796 167 0.863 0.843
0.0709 141 0.891 40 0.699 181 0.848 0.844
0.0758 133 0.902 47 0.658 180 0.838 0.845
0.0806 140 0.884 38 0.816 178 0.870 0.846
0.0855 145 0.875 40 0.762 185 0.851 0.847
0.0904 152 0.856 42 0.741 194 0.831 0.848
0.0952 151 0.876 41 0.735 192 0.846 0.849
$$
Resolution limits = 46.932 3.200
Number of used reflections = 2799
Percentage observed = 99.8303
Percentage of free reflections = 4.8606
Overall R factor = 0.4435
Free R factor = 0.5000
Overall weighted R factor = 0.4392
Free weighted R factor = 0.4651
Overall correlation coefficient = 0.5028
Free correlation coefficient = 0.3590
DPI based on free R factor = 1.0380
Overall figure of merit = 0.8772
ML based su of positional parameters = 0.9914
ML based su of thermal parameters = 54.7370
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Not converging with gamma equal 0.0000000E+00
Trying gamma equal 5.5000003E-02
Gamma decreased to 4.4000003E-02
CGMAT cycle number = 2
weigth matrix 0.1000000
special position ----------- 3.612395
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.063 0.022
Bond angles : refined atoms 1568 4.546 1.952
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.504, B = -11.506
Partial structure 1: scale = 0.294, B = -10.000
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3782
Free R factor = 0.4797
Overall figure of merit = 0.8844
-----------------------------------------------------------------------------
Trying gamma equal 4.4000003E-02
Gamma decreased to 3.4000002E-02
CGMAT cycle number = 3
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.069 0.022
Bond angles : refined atoms 1568 4.618 1.952
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.503, B = -11.736
Partial structure 1: scale = 0.298, B = -9.111
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3564
Free R factor = 0.4762
Overall figure of merit = 0.8857
-----------------------------------------------------------------------------
Trying gamma equal 3.4000002E-02
Gamma decreased to 2.4909092E-02
CGMAT cycle number = 4
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.072 0.022
Bond angles : refined atoms 1568 4.715 1.952
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.503, B = -11.962
Partial structure 1: scale = 0.297, B = -9.771
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3437
Free R factor = 0.4699
Overall figure of merit = 0.8860
-----------------------------------------------------------------------------
Trying gamma equal 2.4909092E-02
Gamma decreased to 1.6644629E-02
CGMAT cycle number = 5
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.073 0.022
Bond angles : refined atoms 1568 4.787 1.952
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.503, B = -12.135
Partial structure 1: scale = 0.298, B = -8.520
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3362
Free R factor = 0.4677
Overall figure of merit = 0.8860
-----------------------------------------------------------------------------
Trying gamma equal 1.6644629E-02
Gamma decreased to 9.1314809E-03
CGMAT cycle number = 6
weigth matrix 9.9999994E-02
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.074 0.022
Bond angles : refined atoms 1568 4.826 1.952
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.502, B = -12.606
Partial structure 1: scale = 0.298, B = -6.905
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3302
Free R factor = 0.4636
Overall figure of merit = 0.8861
-----------------------------------------------------------------------------
Trying gamma equal 9.1314809E-03
Gamma decreased to 2.3013467E-03
CGMAT cycle number = 7
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.074 0.022
Bond angles : refined atoms 1568 4.851 1.952
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.505, B = -12.493
Partial structure 1: scale = 0.311, B = -2.434
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3259
Free R factor = 0.4576
Overall figure of merit = 0.8864
-----------------------------------------------------------------------------
Trying gamma equal 2.3013467E-03
Gamma decreased to 0.0000000E+00
CGMAT cycle number = 8
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.074 0.022
Bond angles : refined atoms 1568 4.872 1.952
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.505, B = -12.666
Partial structure 1: scale = 0.312, B = -0.640
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3222
Free R factor = 0.4524
Overall figure of merit = 0.8868
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Gamma decreased to 0.0000000E+00
CGMAT cycle number = 9
weigth matrix 9.9999994E-02
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.073 0.022
Bond angles : refined atoms 1568 4.890 1.952
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.508, B = -12.231
Partial structure 1: scale = 0.312, B = -4.475
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3205
Free R factor = 0.4512
Overall figure of merit = 0.8876
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Gamma decreased to 0.0000000E+00
CGMAT cycle number = 10
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 127 PHE CE1 . - A 127 PHE CZ . mod.= 1.788 id.= 1.382 dev= -0.406 sig.= 0.030
A 137 ASP CB . - A 137 ASP CG . mod.= 1.916 id.= 1.516 dev= -0.400 sig.= 0.025
A 137 ASP C . - A 137 ASP O . mod.= 1.521 id.= 1.231 dev= -0.290 sig.= 0.020
A 145 LYS CB . - A 145 LYS CG . mod.= 1.896 id.= 1.520 dev= -0.376 sig.= 0.030
B 35 UNK C . - B 35 UNK O . mod.= 1.540 id.= 1.231 dev= -0.309 sig.= 0.020
B 35 UNK C . - B 36 UNK N . mod.= 0.765 id.= 1.329 dev= 0.564 sig.= 0.014
B 36 UNK N . - B 36 UNK CA . mod.= 1.769 id.= 1.458 dev= -0.311 sig.= 0.021
B 36 UNK C . - B 36 UNK O . mod.= 1.478 id.= 1.231 dev= -0.247 sig.= 0.020
B 36 UNK C . - B 37 UNK N . mod.= 1.186 id.= 1.329 dev= 0.143 sig.= 0.014
B 37 UNK C . - B 37 UNK O . mod.= 1.660 id.= 1.231 dev= -0.429 sig.= 0.020
B 38 UNK CA . - B 38 UNK C . mod.= 2.086 id.= 1.525 dev= -0.561 sig.= 0.021
B 38 UNK C . - B 39 VAL N . mod.= 1.120 id.= 1.329 dev= 0.209 sig.= 0.014
B 39 VAL N . - B 39 VAL CA . mod.= 1.719 id.= 1.458 dev= -0.261 sig.= 0.021
B 60 LEU CG . - B 60 LEU CD2 . mod.= 2.005 id.= 1.521 dev= -0.484 sig.= 0.033
B 63 UNK N . - B 63 UNK CA . mod.= 1.678 id.= 1.458 dev= -0.220 sig.= 0.021
B 63 UNK C . - B 64 ALA N . mod.= 1.548 id.= 1.329 dev= -0.219 sig.= 0.014
B 92 ARG CG . - B 92 ARG CD . mod.= 1.841 id.= 1.520 dev= -0.321 sig.= 0.030
C 16 UNK CA . - C 16 UNK CB . mod.= 1.865 id.= 1.521 dev= -0.344 sig.= 0.033
C 24 UNK C . - C 24 UNK O . mod.= 0.986 id.= 1.231 dev= 0.245 sig.= 0.020
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 111 PRO CA - A 111 PRO CD mod.= 97.38 id.= 112.00 dev= 14.622 sig.= 1.400
B 36 UNK N - B 36 UNK C mod.= 69.35 id.= 111.20 dev= 41.847 sig.= 2.800
B 37 UNK N - B 37 UNK C mod.= 81.76 id.= 111.20 dev= 29.442 sig.= 2.800
B 65 LYS O - B 66 GLY N mod.= 105.51 id.= 123.00 dev= 17.492 sig.= 1.600
C 25 UNK N - C 25 UNK C mod.= 80.83 id.= 111.20 dev= 30.367 sig.= 2.800
**** Torsion angle outliers ****
Torsion angle deviations from the ideal >10.000Sigma will be monitored
A 118 LEU CA - A 119 ILE CA mod.= 111.01 id.= 180.00 per.= 1 dev= 68.99 sig.= 5.00
A 136 SER CA - A 137 ASP CA mod.=-119.95 id.= 180.00 per.= 1 dev= -60.05 sig.= 5.00
B 35 UNK CA - B 36 UNK CA mod.= 116.07 id.= 180.00 per.= 1 dev= 63.93 sig.= 5.00
B 53 PRO CA - B 54 GLY CA mod.=-124.71 id.= 180.00 per.= 1 dev= -55.29 sig.= 5.00
B 54 GLY CA - B 55 GLY CA mod.=-118.21 id.= 180.00 per.= 1 dev= -61.79 sig.= 5.00
B 90 SER CA - B 91 GLY CA mod.= -99.86 id.= 180.00 per.= 1 dev= -80.14 sig.= 5.00
B 98 UNK CA - B 99 UNK CA mod.=-129.80 id.= 180.00 per.= 1 dev= -50.20 sig.= 5.00
**** Large deviation of atoms from planarity ****
Deviations from the planarity >10.000Sigma will be monitored
Atom: A 111 PRO N deviation= 0.23 sigma.= 0.02
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.082 0.022
Bond angles : refined atoms 1568 5.176 1.952
Torsion angles, period 1. refined 162 18.727 5.000
Torsion angles, period 2. refined 37 39.096 23.514
Torsion angles, period 3. refined 163 24.335 15.000
Torsion angles, period 4. refined 6 22.756 15.000
Chiral centres: refined atoms 191 0.300 0.200
Planar groups: refined atoms 861 0.020 0.020
VDW repulsions: refined atoms 552 0.406 0.200
VDW; torsion: refined atoms 793 0.393 0.200
HBOND: refined atoms 39 0.259 0.200
VDW repulsions; symmetry: refined atoms 82 0.576 0.200
HBOND; symmetry: refined atoms 1 0.134 0.200
M. chain bond B values: refined atoms 855 0.117 1.500
M. chain angle B values: refined atoms 1256 0.155 2.000
S. chain bond B values: refined atoms 367 1.545 3.000
S. chain angle B values: refined atoms 312 1.954 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.505, B = -12.824
Partial structure 1: scale = 0.313, B = -1.678
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
**** Things for loggraph, R factor and others ****
$TABLE: Cycle 10. Rfactor analysis, F distribution v resln :
$GRAPHS:Cycle 10. v. resln :N:1,6,7,11,12:
:Cycle 10. and v. resln :N:1,4,5,9,10:
:Cycle 10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.003 46 96.23 528.6 428.2 0.48 0.54 5 616.2 516.3 0.54 0.59
0.008 70 98.63 786.7 678.0 0.36 0.41 2 461.7 48.4 0.90 0.86
0.013 80 100.00 715.4 602.5 0.34 0.35 9 607.5 468.2 0.34 0.34
0.017 93 100.00 509.2 535.0 0.35 0.35 6 547.4 392.2 0.57 0.58
0.022 102 100.00 491.7 491.6 0.38 0.39 4 674.7 551.2 0.37 0.41
0.027 129 100.00 511.3 495.4 0.40 0.40 2 790.4 532.1 0.39 0.39
0.032 112 98.41 506.7 474.1 0.45 0.44 12 573.6 447.2 0.52 0.50
0.037 125 100.00 648.7 621.1 0.35 0.36 9 690.5 567.1 0.51 0.49
0.042 141 100.00 716.5 672.5 0.31 0.31 5 823.1 472.9 0.43 0.43
0.047 148 100.00 694.7 637.7 0.31 0.33 3 633.2 385.3 0.46 0.37
0.051 159 100.00 696.9 652.3 0.28 0.28 6 843.7 689.4 0.30 0.29
0.056 159 100.00 786.8 703.6 0.27 0.27 4 617.0 595.7 0.58 0.56
0.061 158 100.00 703.4 611.1 0.29 0.29 9 696.5 519.0 0.45 0.40
0.066 167 100.00 623.7 591.6 0.31 0.30 6 680.8 540.4 0.66 0.68
0.071 181 100.00 643.3 583.0 0.31 0.30 5 840.1 767.6 0.33 0.38
0.076 180 100.00 652.2 611.4 0.30 0.29 11 666.3 568.3 0.33 0.37
0.081 178 100.00 626.6 580.5 0.28 0.28 14 499.6 521.2 0.46 0.41
0.085 185 100.00 563.3 555.9 0.30 0.29 8 449.8 401.2 0.61 0.49
0.090 194 100.00 529.4 493.7 0.32 0.29 11 705.1 534.0 0.43 0.40
0.095 192 100.00 556.0 537.9 0.31 0.29 12 403.4 442.3 0.46 0.39
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 10. Fom(-acentric, centric, overall v resln:
$GRAPHS:Cycle 10. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0029 13 0.980 33 0.880 46 0.908 0.885
0.0077 30 0.950 40 0.945 70 0.947 0.885
0.0126 41 0.925 39 0.893 80 0.909 0.884
0.0175 56 0.938 37 0.823 93 0.892 0.884
0.0223 64 0.921 38 0.845 102 0.893 0.884
0.0272 81 0.928 48 0.825 129 0.890 0.884
0.0320 73 0.926 39 0.860 112 0.903 0.883
0.0369 86 0.921 39 0.828 125 0.892 0.883
0.0418 100 0.947 41 0.830 141 0.913 0.883
0.0466 109 0.929 39 0.858 148 0.910 0.883
0.0515 113 0.925 46 0.841 159 0.901 0.883
0.0563 114 0.943 45 0.865 159 0.921 0.882
0.0612 122 0.937 36 0.786 158 0.903 0.882
0.0661 124 0.904 43 0.826 167 0.884 0.882
0.0709 141 0.899 40 0.702 181 0.856 0.882
0.0758 133 0.914 47 0.657 180 0.847 0.882
0.0806 140 0.897 38 0.824 178 0.881 0.882
0.0855 145 0.894 40 0.801 185 0.874 0.882
0.0904 152 0.877 42 0.753 194 0.850 0.881
0.0952 151 0.885 41 0.790 192 0.864 0.881
$$
Resolution limits = 46.932 3.200
Number of used reflections = 2799
Percentage observed = 99.8303
Percentage of free reflections = 4.8606
Overall R factor = 0.3194
Free R factor = 0.4564
Overall weighted R factor = 0.3215
Free weighted R factor = 0.4437
Overall correlation coefficient = 0.7458
Free correlation coefficient = 0.5074
DPI based on free R factor = 0.9476
Overall figure of merit = 0.8869
ML based su of positional parameters = 0.7466
ML based su of thermal parameters = 40.9093
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Gamma decreased to 0.0000000E+00
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 118 LEU C . - A 119 ILE N . mod.= 1.058 id.= 1.329 dev= 0.271 sig.= 0.014
A 119 ILE N . - A 119 ILE CA . mod.= 1.820 id.= 1.458 dev= -0.362 sig.= 0.021
A 119 ILE CA . - A 119 ILE C . mod.= 1.837 id.= 1.525 dev= -0.312 sig.= 0.021
A 119 ILE C . - A 120 ASN N . mod.= 1.530 id.= 1.329 dev= -0.201 sig.= 0.014
A 120 ASN CA . - A 120 ASN C . mod.= 1.242 id.= 1.525 dev= 0.283 sig.= 0.021
A 120 ASN C . - A 120 ASN O . mod.= 0.973 id.= 1.231 dev= 0.258 sig.= 0.020
A 121 ASP CG . - A 121 ASP OD2 . mod.= 1.598 id.= 1.249 dev= -0.349 sig.= 0.019
A 127 PHE CE1 . - A 127 PHE CZ . mod.= 1.795 id.= 1.382 dev= -0.413 sig.= 0.030
A 137 ASP CB . - A 137 ASP CG . mod.= 1.924 id.= 1.516 dev= -0.408 sig.= 0.025
A 137 ASP C . - A 137 ASP O . mod.= 1.517 id.= 1.231 dev= -0.286 sig.= 0.020
A 145 LYS CB . - A 145 LYS CG . mod.= 1.879 id.= 1.520 dev= -0.359 sig.= 0.030
B 35 UNK N . - B 35 UNK CA . mod.= 1.988 id.= 1.491 dev= -0.497 sig.= 0.021
B 35 UNK C . - B 35 UNK O . mod.= 1.540 id.= 1.231 dev= -0.309 sig.= 0.020
B 35 UNK C . - B 36 UNK N . mod.= 1.096 id.= 1.329 dev= 0.233 sig.= 0.014
B 38 UNK CA . - B 38 UNK C . mod.= 1.805 id.= 1.525 dev= -0.280 sig.= 0.021
B 60 LEU CG . - B 60 LEU CD2 . mod.= 1.929 id.= 1.521 dev= -0.408 sig.= 0.033
B 63 UNK C . - B 64 ALA N . mod.= 1.534 id.= 1.329 dev= -0.205 sig.= 0.014
B 65 LYS CD . - B 65 LYS CE . mod.= 2.084 id.= 1.520 dev= -0.564 sig.= 0.030
B 65 LYS CE . - B 65 LYS NZ . mod.= 1.930 id.= 1.489 dev= -0.441 sig.= 0.030
B 65 LYS C . - B 66 GLY N . mod.= 1.826 id.= 1.329 dev= -0.497 sig.= 0.014
B 66 GLY CA . - B 66 GLY C . mod.= 1.754 id.= 1.516 dev= -0.238 sig.= 0.018
B 69 TRP NE1 . - B 69 TRP CE2 . mod.= 1.535 id.= 1.370 dev= -0.165 sig.= 0.011
B 89 GLY N . - B 89 GLY CA . mod.= 1.685 id.= 1.458 dev= -0.227 sig.= 0.021
B 92 ARG CG . - B 92 ARG CD . mod.= 1.876 id.= 1.520 dev= -0.356 sig.= 0.030
C 16 UNK CA . - C 16 UNK CB . mod.= 1.868 id.= 1.521 dev= -0.347 sig.= 0.033
C 23 UNK C . - C 23 UNK O . mod.= 1.444 id.= 1.231 dev= -0.213 sig.= 0.020
C 23 UNK C . - C 24 UNK N . mod.= 1.495 id.= 1.329 dev= -0.166 sig.= 0.014
C 24 UNK C . - C 25 UNK N . mod.= 1.562 id.= 1.329 dev= -0.233 sig.= 0.014
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 107 UNK N - A 107 UNK C mod.= 78.94 id.= 111.20 dev= 32.261 sig.= 2.800
A 118 LEU N - A 118 LEU CB mod.= 91.27 id.= 110.50 dev= 19.226 sig.= 1.700
A 118 LEU CA - A 118 LEU O mod.= 103.70 id.= 120.80 dev= 17.102 sig.= 1.700
A 119 ILE CA - A 120 ASN N mod.= 92.64 id.= 116.20 dev= 23.559 sig.= 2.000
A 119 ILE C - A 120 ASN CA mod.= 100.90 id.= 121.70 dev= 20.805 sig.= 1.800
A 120 ASN CA - A 120 ASN O mod.= 99.49 id.= 120.80 dev= 21.307 sig.= 1.700
B 35 UNK N - B 35 UNK CB mod.= 133.52 id.= 110.40 dev=-23.116 sig.= 1.500
B 65 LYS CG - B 65 LYS CE mod.= 87.48 id.= 111.30 dev= 23.816 sig.= 2.300
B 65 LYS O - B 66 GLY N mod.= 106.62 id.= 123.00 dev= 16.382 sig.= 1.600
B 65 LYS CA - B 66 GLY N mod.= 136.28 id.= 116.20 dev=-20.084 sig.= 2.000
B 66 GLY CA - B 66 GLY O mod.= 149.47 id.= 120.80 dev=-28.674 sig.= 1.700
C 25 UNK N - C 25 UNK C mod.= 82.47 id.= 111.20 dev= 28.734 sig.= 2.800
**** Torsion angle outliers ****
Torsion angle deviations from the ideal >10.000Sigma will be monitored
A 118 LEU CA - A 119 ILE CA mod.= 118.93 id.= 180.00 per.= 1 dev= 61.07 sig.= 5.00
A 136 SER CA - A 137 ASP CA mod.=-119.72 id.= 180.00 per.= 1 dev= -60.28 sig.= 5.00
B 35 UNK CA - B 36 UNK CA mod.= 117.71 id.= 180.00 per.= 1 dev= 62.29 sig.= 5.00
B 53 PRO CA - B 54 GLY CA mod.=-125.50 id.= 180.00 per.= 1 dev= -54.50 sig.= 5.00
B 54 GLY CA - B 55 GLY CA mod.=-119.84 id.= 180.00 per.= 1 dev= -60.16 sig.= 5.00
B 90 SER CA - B 91 GLY CA mod.= -99.24 id.= 180.00 per.= 1 dev= -80.76 sig.= 5.00
**** Large deviation of atoms from planarity ****
Deviations from the planarity >10.000Sigma will be monitored
Atom: A 111 PRO N deviation= 0.23 sigma.= 0.02
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1154 0.087 0.022
Bond angles : refined atoms 1568 5.566 1.952
Torsion angles, period 1. refined 162 19.402 5.000
Torsion angles, period 2. refined 37 39.300 23.514
Torsion angles, period 3. refined 163 24.091 15.000
Torsion angles, period 4. refined 6 25.144 15.000
Chiral centres: refined atoms 191 0.283 0.200
Planar groups: refined atoms 861 0.024 0.020
VDW repulsions: refined atoms 562 0.418 0.200
VDW; torsion: refined atoms 779 0.393 0.200
HBOND: refined atoms 39 0.293 0.200
VDW repulsions; symmetry: refined atoms 75 0.565 0.200
HBOND; symmetry: refined atoms 1 0.085 0.200
M. chain bond B values: refined atoms 857 0.090 1.500
M. chain angle B values: refined atoms 1256 0.124 2.000
S. chain bond B values: refined atoms 365 1.340 3.000
S. chain angle B values: refined atoms 312 1.822 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.510, B = -12.100
Partial structure 1: scale = 0.312, B = -8.977
Overall anisotropic scale factors
B11 = 0.01 B22 = 0.01 B33 = -0.03 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
**** Things for loggraph, R factor and others ****
$TABLE: Cycle 11. Rfactor analysis, F distribution v resln :
$GRAPHS:Cycle 11. v. resln :N:1,6,7,11,12:
:Cycle 11. and v. resln :N:1,4,5,9,10:
:Cycle 11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.003 46 96.23 524.1 428.4 0.47 0.53 5 610.8 527.1 0.54 0.60
0.008 70 98.63 779.9 674.7 0.36 0.41 2 457.7 30.3 0.93 0.91
0.013 80 100.00 709.2 601.4 0.34 0.35 9 602.3 453.5 0.35 0.36
0.017 93 100.00 504.8 533.4 0.37 0.36 6 542.7 387.9 0.47 0.49
0.022 102 100.00 487.4 497.5 0.41 0.42 4 668.8 531.0 0.38 0.43
0.027 129 100.00 506.9 495.4 0.42 0.42 2 783.6 531.5 0.43 0.46
0.032 112 98.41 502.3 470.2 0.43 0.42 12 568.6 445.0 0.53 0.51
0.037 125 100.00 643.1 619.8 0.33 0.34 9 684.6 562.0 0.55 0.53
0.042 141 100.00 710.3 649.7 0.32 0.33 5 816.0 431.9 0.47 0.48
0.047 148 100.00 688.7 627.0 0.31 0.33 3 627.8 361.4 0.47 0.29
0.051 159 100.00 690.9 634.4 0.29 0.30 6 836.4 689.2 0.27 0.26
0.056 159 100.00 780.0 702.2 0.27 0.27 4 611.7 568.3 0.48 0.47
0.061 158 100.00 697.3 601.3 0.31 0.30 9 690.5 535.0 0.50 0.42
0.066 167 100.00 618.4 581.3 0.31 0.31 6 675.0 573.9 0.59 0.61
0.071 181 100.00 637.7 583.7 0.33 0.32 5 832.9 784.3 0.34 0.39
0.076 180 100.00 646.6 615.1 0.31 0.30 11 660.6 620.4 0.34 0.37
0.081 178 100.00 621.2 577.1 0.28 0.28 14 495.2 509.8 0.44 0.38
0.085 185 100.00 558.5 550.7 0.32 0.31 8 445.9 372.1 0.67 0.55
0.090 194 100.00 524.8 488.3 0.33 0.31 11 699.0 522.9 0.47 0.46
0.095 192 100.00 551.2 527.3 0.31 0.31 12 399.9 416.5 0.41 0.34
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 11. Fom(-acentric, centric, overall v resln:
$GRAPHS:Cycle 11. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0029 13 0.980 33 0.880 46 0.908 0.883
0.0077 30 0.947 40 0.944 70 0.945 0.883
0.0126 41 0.927 39 0.893 80 0.911 0.883
0.0175 56 0.938 37 0.829 93 0.895 0.884
0.0223 64 0.922 38 0.850 102 0.895 0.884
0.0272 81 0.929 48 0.830 129 0.892 0.884
0.0320 73 0.926 39 0.858 112 0.903 0.884
0.0369 86 0.920 39 0.825 125 0.890 0.884
0.0418 100 0.947 41 0.831 141 0.913 0.884
0.0466 109 0.929 39 0.864 148 0.912 0.884
0.0515 113 0.924 46 0.840 159 0.900 0.884
0.0563 114 0.944 45 0.867 159 0.922 0.885
0.0612 122 0.937 36 0.789 158 0.904 0.885
0.0661 124 0.903 43 0.818 167 0.881 0.885
0.0709 141 0.900 40 0.697 181 0.855 0.885
0.0758 133 0.914 47 0.656 180 0.847 0.885
0.0806 140 0.901 38 0.826 178 0.885 0.885
0.0855 145 0.897 40 0.797 185 0.876 0.885
0.0904 152 0.879 42 0.760 194 0.853 0.885
0.0952 151 0.883 41 0.807 192 0.866 0.885
$$
Resolution limits = 46.932 3.200
Number of used reflections = 2799
Percentage observed = 99.8303
Percentage of free reflections = 4.8606
Overall R factor = 0.3264
Free R factor = 0.4581
Overall weighted R factor = 0.3301
Free weighted R factor = 0.4436
Overall correlation coefficient = 0.7417
Free correlation coefficient = 0.5118
DPI based on free R factor = 0.9509
Overall figure of merit = 0.8877
ML based su of positional parameters = 0.7466
ML based su of thermal parameters = 40.9093
-----------------------------------------------------------------------------
Time in seconds: CPU = 5.34
Elapsed = 6.00
**** 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:
$$
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$
$$
0 0.443 0.500 0.877 1296.8 0.055 4.884 0.179
1 0.378 0.480 0.884 642.8 0.063 4.546 0.209
2 0.356 0.476 0.886 439.1 0.069 4.618 0.258
3 0.344 0.470 0.886 323.4 0.072 4.715 0.267
4 0.336 0.468 0.886 257.8 0.073 4.787 0.259
5 0.330 0.464 0.886 223.0 0.074 4.826 0.259
6 0.326 0.458 0.886 165.7 0.074 4.851 0.260
7 0.322 0.452 0.887 129.1 0.074 4.872 0.260
8 0.321 0.451 0.888 86.6 0.073 4.890 0.259
9 0.319 0.456 0.887 121.7 0.082 5.176 0.300
10 0.326 0.458 0.888 111.4 0.087 5.566 0.283
$$
Refmac_5.3.0037: End of Refmac_5.3.0037 Times: User: 7.5s System: 0.3s Elapsed: 0:09
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
Result:
175 residues were built in 3 chains, the longest having 84 residues. 141 residues were sequenced, after pruning.
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
############################################################### ############################################################### ############################################################### ### CCP4 6.0: cbuccaneer version 1.0.0 : 04/10/07## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:11:37 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.
Copyright 2002-2007 Kevin Cowtan and University of York.
$TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$
title [No title given] pdbin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.mtz colin-ref-fo /*/*/[FP.F_sigF.F,FP.F_sigF.sigF] colin-ref-hl /*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D] seqin-wrk /home/cowtan/test/1vjf.seq mtzin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz colin-wrk-fo /*/*/[FP,SIGFP] colin-wrk-free /*/*/[FreeR_flag] colin-wrk-phifom /*/*/[PHCOMB,FOM] pdbin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb pdbout-wrk /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb find grow join link sequence correct filter ncsbuild prune rebuild cycles 1 correlation-mode sequence-reliability 0.95 new-residue-name UNK resolution 2.0 Cycle: 1 C-alphas after finding: 189 C-alphas after growing: 355 C-alphas after joining: 213 C-alphas linked: 0 C-alphas sequenced: 149 C-alphas corrected: 2 C-alphas after filtering: 210 C-alphas after NCS build: 210 C-alphas after pruning: 175 C-alphas after rebuilding: 175
Internal cycle 1 175 residues were built in 3 chains, the longest having 84 residues. 141 residues were sequenced, after pruning.
$TEXT:Result: $$ $$ 175 residues were built in 3 chains, the longest having 84 residues. 141 residues were sequenced, after pruning. $$
cbuccaneer: Normal termination Times: User: 110.4s System: 0.3s Elapsed: 1:50
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
| Initial | After 10 cycles | |
|---|---|---|
| R factor | 0.390 | 0.274 |
| Rfree | 0.441 | 0.386 |
|
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 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. 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 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. 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_5.3.0037 version 5.3.0037 : 03/29/06## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:13:27 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--- title [No title given]
TITL
Data line--- weight MATRIX 0.1
WEIG
Data line--- labin HLA=pirate.ABCD.A HLB=pirate.ABCD.B HLC=pirate.ABCD.C HLD=pirate.ABCD.D FREE=FreeR_flag FP=FP SIGFP=SIGFP
LABI
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 PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT
REFI
Data line--- ncyc 10
NCYC
Data line--- scal type SIMP LSSC ANISO EXPE
SCAL
Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
SOLV
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--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
LABO
Data line--- PNAME buccaneer
PNAM
Data line--- DNAME buccaneer
DNAM
Data line--- RSIZE 80
RSIZ
Data line--- END
END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /home/cowtan/test/1vjf-3.2A.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name - /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
Input reflection file. Logical name - HKLIN actual file name - /home/cowtan/test/1vjf-3.2A.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
Cell from mtz : 50.903 50.903 121.411 90.000 90.000 90.000
Space group from mtz: number - 96; name - P43212
Refinement type : Restrained
**** Makecif parameters ****
Dictionary files for restraints : /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/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 : Phase modified Maximum Likelihood for Fs
Phase Blurred by Scale*Exp(-B s**2) : 1.00 0.00
**** 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 1.400
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 0.0049
Refinement of individual isotropic Bfactors
Refinement resln : 46.9323 3.2002
Estimated number of reflections : 3404
Free R exclusion - flag equals: 0
Weighting by comparison of trace of matrix
Weighting parameters : 0.1000
Refinement cycles : 10
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
Input phases not used in SigmaA estimation
Scaling and SigmaA resln: 46.9323 3.2002
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/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.12
_lib_update 20/09/07
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2436
with complete description : 454
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: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/atomsf.lib
Number of atoms : 1236
Number of residues : 175
Number of chains : 3
I am reading library. Please wait.
mon_lib.cif
INFO: link is found (not be used) dist= 1.447 ideal_dist= 1.450
ch:AA res: 97 UNK at:N .->ch:AA res: 124 ARG at:CG .
INFO: link is found (not be used) dist= 0.948 ideal_dist= 1.450
ch:AA res: 97 UNK at:N .->ch:AA res: 124 ARG at:CD .
INFO: link is found (not be used) dist= 1.290 ideal_dist= 1.524
ch:AA res: 97 UNK at:CA .->ch:AA res: 124 ARG at:CD .
INFO: link is found (not be used) dist= 1.643 ideal_dist= 1.510
ch:AA res: 97 UNK at:C .->ch:AA res: 124 ARG at:CD .
INFO: link is found (not be used) dist= 0.991 ideal_dist= 1.339
ch:AA res: 97 UNK at:C .->ch:AA res: 124 ARG at:NE .
INFO: link is found (not be used) dist= 1.589 ideal_dist= 1.460
ch:AA res: 97 UNK at:C .->ch:AA res: 124 ARG at:CZ .
INFO: link is found (not be used) dist= 1.146 ideal_dist= 1.240
ch:AA res: 97 UNK at:O .->ch:AA res: 124 ARG at:NE .
INFO: link is found (not be used) dist= 0.881 ideal_dist= 1.330
ch:AA res: 97 UNK at:O .->ch:AA res: 124 ARG at:CZ .
INFO: link is found (not be used) dist= 1.207 ideal_dist= 1.240
ch:AA res: 97 UNK at:O .->ch:AA res: 124 ARG at:NH1 .
INFO: link is found (not be used) dist= 1.275 ideal_dist= 1.337
ch:AA res: 99 UNK at:CB .->ch:AA res: 103 GLU at:OE1 .
INFO: link is found (not be used) dist= 1.666 ideal_dist= 1.420
ch:AA res: 111 SER at:CB .->ch:AA res: 146 ASN at:OD1 .
INFO: link is found (not be used) dist= 1.365 ideal_dist= 1.462
ch:AA res: 124 ARG at:NH1 .->ch:BB res: 68 LEU at:CD1 .
INFO: link is found (not be used) dist= 1.396 ideal_dist= 1.337
ch:BB res: 40 ARG at:CG .->ch:BB res: 42 GLU at:OE1 .
INFO: link is found (not be used) dist= 1.515 ideal_dist= 1.337
ch:BB res: 40 ARG at:CD .->ch:BB res: 42 GLU at:OE1 .
INFO: link is found (not be used) dist= 1.289 ideal_dist= 1.339
ch:BB res: 40 ARG at:NE .->ch:BB res: 42 GLU at:CD .
INFO: link is found (not be used) dist= 1.479 ideal_dist= 1.275
ch:BB res: 40 ARG at:NE .->ch:BB res: 42 GLU at:OE1 .
INFO: link is found (not be used) dist= 0.773 ideal_dist= 1.510
ch:BB res: 40 ARG at:CZ .->ch:BB res: 42 GLU at:CG .
INFO: link is found (not be used) dist= 1.181 ideal_dist= 1.460
ch:BB res: 40 ARG at:CZ .->ch:BB res: 42 GLU at:CD .
INFO: link is found (not be used) dist= 0.497 ideal_dist= 1.457
ch:BB res: 40 ARG at:NH1 .->ch:BB res: 42 GLU at:CB .
INFO: link is found (not be used) dist= 1.076 ideal_dist= 1.457
ch:BB res: 40 ARG at:NH1 .->ch:BB res: 42 GLU at:CG .
INFO: link is found (not be used) dist= 1.278 ideal_dist= 1.457
ch:BB res: 40 ARG at:NH2 .->ch:BB res: 42 GLU at:CG .
INFO: link is found (not be used) dist= 1.416 ideal_dist= 1.275
ch:BB res: 63 ASP at:OD1 .->ch:BB res: 67 GLN at:N .
INFO: link is found (not be used) dist= 1.628 ideal_dist= 1.413
ch:BB res: 35 UNK at:CB .->ch:CC res: 24 UNK at:O .
--------------------------------
--- title of input coord file ---
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-XX
--------------------------------
ATTENTION: atom:O UNK 180 AA is missing in the structure
ATTENTION: atom:O GLN 98 BB is missing in the structure
ATTENTION: atom:O UNK 26 CC is missing in the structure
Number of chains : 3
Total number of monomers : 175
Number of atoms : 1239
Number of missing atoms : 3
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0
Number of bonds restraints : 1254
Number of angles restraints : 1703
Number of torsions restraints : 838
Number of chiralities : 208
Number of planar groups : 221
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 2948
Number of reflection read 2948
CGMAT cycle number = 1
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 99 UNK C . - A 100 UNK N . mod.= 1.170 id.= 1.329 dev= 0.159 sig.= 0.014
A 107 VAL C . - A 108 THR N . mod.= 1.157 id.= 1.329 dev= 0.172 sig.= 0.014
A 108 THR C . - A 109 PRO N . mod.= 1.088 id.= 1.341 dev= 0.253 sig.= 0.016
A 109 PRO N . - A 109 PRO CA . mod.= 1.240 id.= 1.458 dev= 0.218 sig.= 0.021
A 109 PRO CD . - A 109 PRO N . mod.= 1.933 id.= 1.473 dev= -0.460 sig.= 0.014
A 120 ASP CA . - A 120 ASP C . mod.= 1.260 id.= 1.525 dev= 0.265 sig.= 0.021
A 120 ASP C . - A 121 THR N . mod.= 1.139 id.= 1.329 dev= 0.190 sig.= 0.014
B 34 UNK N . - B 34 UNK CA . mod.= 1.987 id.= 1.491 dev= -0.496 sig.= 0.021
B 34 UNK C . - B 35 UNK N . mod.= 1.095 id.= 1.329 dev= 0.234 sig.= 0.014
B 37 PRO CD . - B 37 PRO N . mod.= 2.196 id.= 1.473 dev= -0.723 sig.= 0.014
B 37 PRO CA . - B 37 PRO C . mod.= 1.805 id.= 1.525 dev= -0.280 sig.= 0.021
B 52 PRO CD . - B 52 PRO N . mod.= 1.953 id.= 1.473 dev= -0.480 sig.= 0.014
B 56 THR N . - B 56 THR CA . mod.= 1.245 id.= 1.458 dev= 0.213 sig.= 0.021
B 56 THR C . - B 57 LYS N . mod.= 1.186 id.= 1.329 dev= 0.143 sig.= 0.014
B 65 LYS C . - B 66 GLY N . mod.= 0.983 id.= 1.329 dev= 0.346 sig.= 0.014
B 75 GLY C . - B 76 GLU N . mod.= 1.181 id.= 1.329 dev= 0.148 sig.= 0.014
B 89 GLY N . - B 89 GLY CA . mod.= 1.684 id.= 1.458 dev= -0.226 sig.= 0.021
C 12 UNK C . - C 13 UNK N . mod.= 1.112 id.= 1.329 dev= 0.217 sig.= 0.014
C 20 UNK C . - C 21 UNK N . mod.= 1.006 id.= 1.329 dev= 0.323 sig.= 0.014
C 21 UNK C . - C 22 UNK N . mod.= 1.060 id.= 1.329 dev= 0.269 sig.= 0.014
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 106 GLY O - A 107 VAL N mod.= 94.73 id.= 123.00 dev= 28.266 sig.= 1.600
A 106 GLY CA - A 107 VAL N mod.= 144.33 id.= 116.20 dev=-28.132 sig.= 2.000
A 106 GLY C - A 107 VAL CA mod.= 145.83 id.= 121.70 dev=-24.129 sig.= 1.800
A 107 VAL O - A 108 THR N mod.= 99.42 id.= 123.00 dev= 23.579 sig.= 1.600
A 107 VAL CA - A 108 THR N mod.= 139.62 id.= 116.20 dev=-23.421 sig.= 2.000
A 108 THR C - A 109 PRO CD mod.= 68.32 id.= 125.00 dev= 56.682 sig.= 4.100
A 109 PRO N - A 109 PRO CG mod.= 78.82 id.= 103.20 dev= 24.380 sig.= 1.500
A 120 ASP O - A 121 THR N mod.= 100.87 id.= 123.00 dev= 22.132 sig.= 1.600
A 120 ASP CA - A 121 THR N mod.= 138.24 id.= 116.20 dev=-22.039 sig.= 2.000
B 37 PRO CA - B 37 PRO CD mod.= 81.71 id.= 112.00 dev= 30.292 sig.= 1.400
B 37 PRO N - B 37 PRO CG mod.= 79.63 id.= 103.20 dev= 23.565 sig.= 1.500
B 52 PRO CA - B 52 PRO CD mod.= 88.44 id.= 112.00 dev= 23.556 sig.= 1.400
B 52 PRO N - B 52 PRO CG mod.= 81.54 id.= 103.20 dev= 21.657 sig.= 1.500
B 67 GLN N - B 67 GLN C mod.= 150.46 id.= 111.20 dev=-39.264 sig.= 2.800
C 25 UNK N - C 25 UNK C mod.= 82.46 id.= 111.20 dev= 28.740 sig.= 2.800
**** Torsion angle outliers ****
Torsion angle deviations from the ideal >10.000Sigma will be monitored
A 136 SER CA - A 137 ASP CA mod.=-119.67 id.= 180.00 per.= 1 dev= -60.33 sig.= 5.00
B 34 UNK CA - B 35 UNK CA mod.= 117.72 id.= 180.00 per.= 1 dev= 62.28 sig.= 5.00
B 52 PRO CA - B 53 GLY CA mod.=-125.50 id.= 180.00 per.= 1 dev= -54.50 sig.= 5.00
B 53 GLY CA - B 54 GLY CA mod.=-119.90 id.= 180.00 per.= 1 dev= -60.10 sig.= 5.00
B 90 SER CA - B 91 GLY CA mod.= -99.30 id.= 180.00 per.= 1 dev= -80.70 sig.= 5.00
**** Large deviation of atoms from planarity ****
Deviations from the planarity >10.000Sigma will be monitored
Atom: A 108 THR C deviation= 0.21 sigma.= 0.02
Atom: A 109 PRO N deviation= -0.38 sigma.= 0.02
Atom: B 36 UNK C deviation= 0.20 sigma.= 0.02
Atom: B 37 PRO N deviation= -0.44 sigma.= 0.02
Atom: B 52 PRO N deviation= -0.26 sigma.= 0.02
**** VDW outliers ****
VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored
A 97 UNK N . - A 124 ARG CG . mod.= 1.447 id.= 3.520 dev= -2.07 sig.= 0.20 sym.= 1 0 0 0
A 97 UNK N . - A 124 ARG CD . mod.= 0.948 id.= 3.520 dev= -2.57 sig.= 0.20 sym.= 1 0 0 0
A 97 UNK CA . - A 124 ARG CD . mod.= 1.290 id.= 3.870 dev= -2.58 sig.= 0.20 sym.= 1 0 0 0
A 97 UNK C . - A 124 ARG CD . mod.= 1.643 id.= 3.670 dev= -2.03 sig.= 0.20 sym.= 1 0 0 0
A 97 UNK C . - A 124 ARG NE . mod.= 0.991 id.= 3.350 dev= -2.36 sig.= 0.20 sym.= 1 0 0 0
A 97 UNK O . - A 124 ARG CZ . mod.= 0.881 id.= 3.270 dev= -2.39 sig.= 0.20 sym.= 1 0 0 0
A 99 UNK CB . - A 103 GLU OE1 . mod.= 1.275 id.= 3.460 dev= -2.19 sig.= 0.20 sym.= 1 0 0 0
A 105 LEU CD2 . - A 117 LEU CD2 . mod.= 1.792 id.= 3.880 dev= -2.09 sig.= 0.20 sym.= 1 0 0 0
A 124 ARG NH1 . - B 68 LEU CD1 . mod.= 1.365 id.= 3.540 dev= -2.18 sig.= 0.20 sym.= 1 0 0 0
A 137 ASP OD1 . - A 138 PRO CD . mod.= 0.788 id.= 3.440 dev= -2.65 sig.= 0.20 sym.= 1 0 0 0
B 40 ARG CG . - B 42 GLU OE1 . mod.= 1.396 id.= 3.440 dev= -2.04 sig.= 0.20 sym.= 1 0 0 0
B 40 ARG NE . - B 42 GLU CD . mod.= 1.289 id.= 3.350 dev= -2.06 sig.= 0.20 sym.= 1 0 0 0
B 40 ARG CZ . - B 42 GLU CG . mod.= 0.773 id.= 3.670 dev= -2.90 sig.= 0.20 sym.= 1 0 0 0
B 40 ARG CZ . - B 42 GLU CD . mod.= 1.181 id.= 3.500 dev= -2.32 sig.= 0.20 sym.= 1 0 0 0
B 40 ARG NH1 . - B 42 GLU CG . mod.= 1.076 id.= 3.520 dev= -2.44 sig.= 0.20 sym.= 1 0 0 0
B 40 ARG NH1 . - B 42 GLU CB . mod.= 0.497 id.= 3.520 dev= -3.02 sig.= 0.20 sym.= 1 0 0 0
B 40 ARG NH2 . - B 42 GLU CG . mod.= 1.278 id.= 3.520 dev= -2.24 sig.= 0.20 sym.= 1 0 0 0
weigth matrix 0.1000000
special position ----------- 3.193648
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.050 0.022
Bond angles : refined atoms 1703 4.403 1.960
Torsion angles, period 1. refined 172 15.113 5.000
Torsion angles, period 2. refined 42 37.997 24.048
Torsion angles, period 3. refined 189 6.834 15.000
Torsion angles, period 4. refined 6 5.919 15.000
Chiral centres: refined atoms 208 0.179 0.200
Planar groups: refined atoms 928 0.025 0.020
VDW repulsions: refined atoms 865 0.654 0.200
VDW; torsion: refined atoms 867 0.362 0.200
HBOND: refined atoms 53 0.563 0.200
VDW repulsions; symmetry: refined atoms 42 0.457 0.200
M. chain bond B values: refined atoms 863 0.000 1.500
M. chain angle B values: refined atoms 1350 0.000 2.000
S. chain bond B values: refined atoms 391 0.000 3.000
S. chain angle B values: refined atoms 353 0.000 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.480, B = -47.873
Partial structure 1: scale = 0.311, B = 21.740
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
**** Things for loggraph, R factor and others ****
$TABLE: Cycle 1. Rfactor analysis, F distribution v resln :
$GRAPHS:Cycle 1. 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.003 46 96.23 556.8 466.7 0.44 0.52 5 649.0 553.1 0.28 0.32
0.008 70 98.63 828.7 640.4 0.34 0.36 2 486.3 163.4 0.66 0.53
0.013 80 100.00 753.5 689.7 0.33 0.34 9 639.9 540.4 0.46 0.54
0.017 93 100.00 536.3 505.4 0.34 0.34 6 576.6 442.6 0.38 0.37
0.022 102 100.00 517.9 499.2 0.45 0.46 4 710.6 514.3 0.62 0.50
0.027 129 100.00 538.6 550.6 0.38 0.37 2 832.5 502.4 0.40 0.41
0.032 112 98.41 533.7 556.9 0.49 0.47 12 604.1 504.3 0.40 0.34
0.037 125 100.00 683.3 641.1 0.38 0.38 9 727.4 636.5 0.44 0.37
0.042 141 100.00 754.7 735.3 0.35 0.36 5 867.0 668.5 0.23 0.27
0.047 148 100.00 731.8 663.1 0.37 0.38 3 667.0 590.6 0.43 0.44
0.051 159 100.00 734.1 667.4 0.35 0.35 6 888.7 650.7 0.27 0.23
0.056 159 100.00 828.8 708.4 0.33 0.34 4 649.9 603.1 0.56 0.55
0.061 158 100.00 740.9 607.3 0.37 0.36 9 733.7 360.5 0.58 0.57
0.066 167 100.00 657.0 556.8 0.41 0.40 6 717.1 525.8 0.44 0.44
0.071 181 100.00 677.6 578.2 0.42 0.40 5 884.9 582.9 0.40 0.41
0.076 180 100.00 687.0 591.7 0.41 0.40 11 701.9 538.2 0.42 0.47
0.081 178 100.00 660.0 598.2 0.38 0.37 14 526.2 535.4 0.49 0.47
0.085 185 100.00 593.4 546.2 0.44 0.42 8 473.7 431.4 0.74 0.61
0.090 194 100.00 557.6 503.9 0.44 0.43 11 742.7 517.0 0.39 0.40
0.095 192 100.00 585.6 569.2 0.41 0.40 12 424.9 357.5 0.46 0.43
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0029 13 0.980 33 0.925 46 0.941 0.895
0.0077 30 0.948 40 0.941 70 0.944 0.892
0.0126 41 0.922 39 0.879 80 0.901 0.890
0.0175 56 0.934 37 0.797 93 0.880 0.889
0.0223 64 0.919 38 0.839 102 0.889 0.888
0.0272 81 0.932 48 0.837 129 0.897 0.887
0.0320 73 0.926 39 0.870 112 0.906 0.885
0.0369 86 0.916 39 0.864 125 0.900 0.884
0.0418 100 0.945 41 0.843 141 0.915 0.884
0.0466 109 0.929 39 0.833 148 0.904 0.883
0.0515 113 0.920 46 0.824 159 0.892 0.882
0.0563 114 0.934 45 0.902 159 0.925 0.881
0.0612 122 0.928 36 0.798 158 0.899 0.880
0.0661 124 0.895 43 0.825 167 0.877 0.880
0.0709 141 0.898 40 0.720 181 0.859 0.879
0.0758 133 0.906 47 0.655 180 0.841 0.878
0.0806 140 0.892 38 0.806 178 0.874 0.878
0.0855 145 0.886 40 0.754 185 0.857 0.877
0.0904 152 0.869 42 0.747 194 0.843 0.876
0.0952 151 0.878 41 0.798 192 0.861 0.876
$$
Resolution limits = 46.932 3.200
Number of used reflections = 2799
Percentage observed = 99.8303
Percentage of free reflections = 4.8606
Overall R factor = 0.3896
Free R factor = 0.4406
Overall weighted R factor = 0.3885
Free weighted R factor = 0.4340
Overall correlation coefficient = 0.6297
Free correlation coefficient = 0.5329
DPI based on free R factor = 0.9531
Overall figure of merit = 0.8837
ML based su of positional parameters = 0.8548
ML based su of thermal parameters = 47.1747
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 2
weigth matrix 0.1000000
special position ----------- 3.340322
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.065 0.022
Bond angles : refined atoms 1703 5.299 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.483, B = -13.479
Partial structure 1: scale = 0.311, B = -6.884
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3314
Free R factor = 0.4055
Overall figure of merit = 0.8893
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Not converging with gamma equal 0.0000000E+00
Trying gamma equal 5.5000003E-02
Gamma decreased to 4.4000003E-02
CGMAT cycle number = 3
weigth matrix 0.1000000
special position ----------- 3.866606
special position ----------- 3.413604
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.061 0.022
Bond angles : refined atoms 1703 4.758 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.483, B = -13.581
Partial structure 1: scale = 0.312, B = -1.015
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.3105
Free R factor = 0.3929
Overall figure of merit = 0.8917
-----------------------------------------------------------------------------
Trying gamma equal 4.4000003E-02
Gamma decreased to 3.4000002E-02
CGMAT cycle number = 4
weigth matrix 9.9999994E-02
special position ----------- 3.785506
special position ----------- 3.482043
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.062 0.022
Bond angles : refined atoms 1703 4.654 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.484, B = -13.679
Partial structure 1: scale = 0.312, B = -0.111
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2993
Free R factor = 0.3864
Overall figure of merit = 0.8933
-----------------------------------------------------------------------------
Trying gamma equal 3.4000002E-02
Gamma decreased to 2.4909092E-02
CGMAT cycle number = 5
weigth matrix 0.1000000
special position ----------- 3.820793
special position ----------- 3.556735
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.063 0.022
Bond angles : refined atoms 1703 4.614 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.484, B = -13.938
Partial structure 1: scale = 0.310, B = 1.072
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2925
Free R factor = 0.3862
Overall figure of merit = 0.8941
-----------------------------------------------------------------------------
Trying gamma equal 2.4909092E-02
Gamma decreased to 1.6644629E-02
CGMAT cycle number = 6
weigth matrix 0.1000000
special position ----------- 3.717989
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.063 0.022
Bond angles : refined atoms 1703 4.574 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.484, B = -14.011
Partial structure 1: scale = 0.310, B = 0.654
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2874
Free R factor = 0.3847
Overall figure of merit = 0.8947
-----------------------------------------------------------------------------
Trying gamma equal 1.6644629E-02
Gamma decreased to 9.1314809E-03
CGMAT cycle number = 7
weigth matrix 0.1000000
special position ----------- 3.892307
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.062 0.022
Bond angles : refined atoms 1703 4.537 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.484, B = -14.207
Partial structure 1: scale = 0.310, B = 1.120
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2835
Free R factor = 0.3827
Overall figure of merit = 0.8949
-----------------------------------------------------------------------------
Trying gamma equal 9.1314809E-03
Gamma decreased to 2.3013467E-03
CGMAT cycle number = 8
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.062 0.022
Bond angles : refined atoms 1703 4.500 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.485, B = -14.339
Partial structure 1: scale = 0.310, B = 2.082
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2801
Free R factor = 0.3849
Overall figure of merit = 0.8950
-----------------------------------------------------------------------------
Trying gamma equal 2.3013467E-03
Not converging with gamma equal 2.3013467E-03
Trying gamma equal 3.6452018E-02
Gamma decreased to 2.9621884E-02
CGMAT cycle number = 9
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.062 0.022
Bond angles : refined atoms 1703 4.462 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.485, B = -14.313
Partial structure 1: scale = 0.308, B = 0.494
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2781
Free R factor = 0.3841
Overall figure of merit = 0.8953
-----------------------------------------------------------------------------
Trying gamma equal 2.9621884E-02
Gamma decreased to 2.3412671E-02
CGMAT cycle number = 10
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 137 ASP C . - A 138 PRO N . mod.= 1.517 id.= 1.341 dev= -0.176 sig.= 0.016
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 106 GLY C - A 107 VAL CA mod.= 101.87 id.= 121.70 dev= 19.833 sig.= 1.800
A 107 VAL N - A 107 VAL C mod.= 141.06 id.= 111.20 dev=-29.859 sig.= 2.800
**** Torsion angle outliers ****
Torsion angle deviations from the ideal >10.000Sigma will be monitored
A 137 ASP CA - A 138 PRO CA mod.= 114.58 id.= 180.00 per.= 1 dev= 65.42 sig.= 5.00
B 34 UNK CA - B 35 UNK CA mod.= 120.39 id.= 180.00 per.= 1 dev= 59.61 sig.= 5.00
B 52 PRO CA - B 53 GLY CA mod.=-123.26 id.= 180.00 per.= 1 dev= -56.74 sig.= 5.00
B 90 SER CA - B 91 GLY CA mod.= -93.50 id.= 180.00 per.= 1 dev= -86.50 sig.= 5.00
**** Large deviation of atoms from planarity ****
Deviations from the planarity >10.000Sigma will be monitored
Atom: A 109 PRO N deviation= -0.20 sigma.= 0.02
**** VDW outliers ****
VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored
A 137 ASP OD1 . - A 138 PRO CD . mod.= 1.371 id.= 3.440 dev= -2.07 sig.= 0.20 sym.= 1 0 0 0
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.061 0.022
Bond angles : refined atoms 1703 4.427 1.960
Torsion angles, period 1. refined 172 16.779 5.000
Torsion angles, period 2. refined 42 41.314 24.048
Torsion angles, period 3. refined 189 22.708 15.000
Torsion angles, period 4. refined 6 18.244 15.000
Chiral centres: refined atoms 208 0.267 0.200
Planar groups: refined atoms 928 0.016 0.020
VDW repulsions: refined atoms 710 0.462 0.200
VDW; torsion: refined atoms 863 0.388 0.200
HBOND: refined atoms 54 0.340 0.200
VDW repulsions; symmetry: refined atoms 35 0.305 0.200
HBOND; symmetry: refined atoms 1 0.110 0.200
M. chain bond B values: refined atoms 894 0.000 1.500
M. chain angle B values: refined atoms 1350 0.000 2.000
S. chain bond B values: refined atoms 413 0.799 3.000
S. chain angle B values: refined atoms 353 1.473 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.487, B = -13.964
Partial structure 1: scale = 0.308, B = -2.091
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
**** Things for loggraph, R factor and others ****
$TABLE: Cycle 10. Rfactor analysis, F distribution v resln :
$GRAPHS:Cycle 10. v. resln :N:1,6,7,11,12:
:Cycle 10. and v. resln :N:1,4,5,9,10:
:Cycle 10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.003 46 96.23 547.9 470.8 0.39 0.47 5 638.6 521.6 0.38 0.46
0.008 70 98.63 815.4 651.2 0.32 0.35 2 478.5 204.5 0.76 0.64
0.013 80 100.00 741.4 686.9 0.27 0.29 9 629.6 514.2 0.30 0.33
0.017 93 100.00 527.7 517.6 0.32 0.32 6 567.3 397.9 0.45 0.45
0.022 102 100.00 509.5 496.7 0.39 0.40 4 699.2 413.4 0.44 0.36
0.027 129 100.00 530.0 523.8 0.36 0.37 2 819.2 530.4 0.35 0.39
0.032 112 98.41 525.1 536.5 0.38 0.38 12 594.4 490.1 0.41 0.38
0.037 125 100.00 672.3 649.2 0.32 0.33 9 715.7 791.8 0.32 0.31
0.042 141 100.00 742.6 732.5 0.26 0.26 5 853.1 632.6 0.26 0.27
0.047 148 100.00 720.0 677.5 0.24 0.24 3 656.3 451.2 0.69 0.64
0.051 159 100.00 722.3 698.7 0.25 0.25 6 874.4 736.8 0.18 0.17
0.056 159 100.00 815.5 738.6 0.25 0.25 4 639.4 640.4 0.36 0.36
0.061 158 100.00 729.0 664.2 0.25 0.26 9 721.9 390.2 0.51 0.53
0.066 167 100.00 646.4 608.5 0.26 0.27 6 705.6 618.7 0.40 0.37
0.071 181 100.00 666.7 612.3 0.26 0.27 5 870.7 792.7 0.16 0.18
0.076 180 100.00 676.0 625.1 0.26 0.26 11 690.6 569.8 0.39 0.39
0.081 178 100.00 649.4 607.2 0.25 0.25 14 517.7 559.2 0.41 0.39
0.085 185 100.00 583.8 586.7 0.26 0.25 8 466.1 375.7 0.58 0.49
0.090 194 100.00 548.7 527.7 0.27 0.26 11 730.8 582.7 0.35 0.32
0.095 192 100.00 576.2 564.4 0.26 0.25 12 418.0 399.7 0.50 0.47
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 10. Fom(-acentric, centric, overall v resln:
$GRAPHS:Cycle 10. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0029 13 0.981 33 0.905 46 0.926 0.915
0.0077 30 0.954 40 0.950 70 0.952 0.915
0.0126 41 0.927 39 0.888 80 0.908 0.916
0.0175 56 0.937 37 0.825 93 0.892 0.916
0.0223 64 0.928 38 0.855 102 0.901 0.916
0.0272 81 0.934 48 0.843 129 0.900 0.917
0.0320 73 0.934 39 0.869 112 0.911 0.917
0.0369 86 0.927 39 0.860 125 0.906 0.917
0.0418 100 0.953 41 0.843 141 0.921 0.917
0.0466 109 0.938 39 0.865 148 0.918 0.917
0.0515 113 0.928 46 0.838 159 0.902 0.918
0.0563 114 0.947 45 0.904 159 0.935 0.918
0.0612 122 0.941 36 0.837 158 0.917 0.918
0.0661 124 0.910 43 0.824 167 0.888 0.918
0.0709 141 0.913 40 0.737 181 0.874 0.918
0.0758 133 0.924 47 0.652 180 0.853 0.918
0.0806 140 0.905 38 0.829 178 0.889 0.919
0.0855 145 0.901 40 0.799 185 0.879 0.919
0.0904 152 0.885 42 0.788 194 0.864 0.919
0.0952 151 0.894 41 0.795 192 0.873 0.919
$$
Resolution limits = 46.932 3.200
Number of used reflections = 2799
Percentage observed = 99.8303
Percentage of free reflections = 4.8606
Overall R factor = 0.2761
Free R factor = 0.3848
Overall weighted R factor = 0.2830
Free weighted R factor = 0.3781
Overall correlation coefficient = 0.8118
Free correlation coefficient = 0.6305
DPI based on free R factor = 0.8326
Overall figure of merit = 0.8957
ML based su of positional parameters = 0.6276
ML based su of thermal parameters = 34.2870
-----------------------------------------------------------------------------
Trying gamma equal 2.3412671E-02
Gamma decreased to 1.7767932E-02
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 137 ASP C . - A 138 PRO N . mod.= 1.517 id.= 1.341 dev= -0.176 sig.= 0.016
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 98 UNK C - A 99 UNK CA mod.= 103.32 id.= 121.70 dev= 18.377 sig.= 1.800
A 106 GLY C - A 107 VAL CA mod.= 101.45 id.= 121.70 dev= 20.248 sig.= 1.800
A 107 VAL N - A 107 VAL C mod.= 142.08 id.= 111.20 dev=-30.881 sig.= 2.800
**** Torsion angle outliers ****
Torsion angle deviations from the ideal >10.000Sigma will be monitored
A 137 ASP CA - A 138 PRO CA mod.= 114.78 id.= 180.00 per.= 1 dev= 65.22 sig.= 5.00
B 34 UNK CA - B 35 UNK CA mod.= 119.89 id.= 180.00 per.= 1 dev= 60.11 sig.= 5.00
B 52 PRO CA - B 53 GLY CA mod.=-123.53 id.= 180.00 per.= 1 dev= -56.47 sig.= 5.00
B 90 SER CA - B 91 GLY CA mod.= -93.13 id.= 180.00 per.= 1 dev= -86.87 sig.= 5.00
**** VDW outliers ****
VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored
A 137 ASP OD1 . - A 138 PRO CD . mod.= 1.361 id.= 3.440 dev= -2.08 sig.= 0.20 sym.= 1 0 0 0
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1254 0.061 0.022
Bond angles : refined atoms 1703 4.388 1.960
Torsion angles, period 1. refined 172 16.834 5.000
Torsion angles, period 2. refined 42 42.053 24.048
Torsion angles, period 3. refined 189 22.766 15.000
Torsion angles, period 4. refined 6 19.290 15.000
Chiral centres: refined atoms 208 0.271 0.200
Planar groups: refined atoms 928 0.016 0.020
VDW repulsions: refined atoms 705 0.457 0.200
VDW; torsion: refined atoms 862 0.386 0.200
HBOND: refined atoms 55 0.332 0.200
VDW repulsions; symmetry: refined atoms 33 0.317 0.200
HBOND; symmetry: refined atoms 1 0.162 0.200
M. chain bond B values: refined atoms 893 0.000 1.500
M. chain angle B values: refined atoms 1350 0.000 2.000
S. chain bond B values: refined atoms 414 0.783 3.000
S. chain angle B values: refined atoms 353 1.412 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.487, B = -14.084
Partial structure 1: scale = 0.307, B = -0.930
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
**** Things for loggraph, R factor and others ****
$TABLE: Cycle 11. Rfactor analysis, F distribution v resln :
$GRAPHS:Cycle 11. v. resln :N:1,6,7,11,12:
:Cycle 11. and v. resln :N:1,4,5,9,10:
:Cycle 11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.003 46 96.23 547.8 472.6 0.39 0.48 5 638.5 524.6 0.39 0.46
0.008 70 98.63 815.3 655.6 0.32 0.35 2 478.4 212.3 0.74 0.63
0.013 80 100.00 741.4 688.5 0.27 0.29 9 629.6 515.3 0.29 0.32
0.017 93 100.00 527.7 516.7 0.33 0.32 6 567.3 397.4 0.45 0.45
0.022 102 100.00 509.5 499.1 0.39 0.40 4 699.2 410.2 0.44 0.36
0.027 129 100.00 529.9 523.4 0.36 0.37 2 819.1 533.6 0.35 0.39
0.032 112 98.41 525.1 536.4 0.37 0.37 12 594.4 484.6 0.41 0.39
0.037 125 100.00 672.3 650.6 0.31 0.33 9 715.6 798.5 0.32 0.32
0.042 141 100.00 742.5 731.5 0.26 0.26 5 853.0 631.9 0.26 0.27
0.047 148 100.00 719.9 676.3 0.23 0.24 3 656.2 443.0 0.70 0.65
0.051 159 100.00 722.2 697.8 0.25 0.25 6 874.4 735.8 0.18 0.17
0.056 159 100.00 815.4 738.9 0.25 0.25 4 639.4 632.5 0.34 0.34
0.061 158 100.00 728.9 665.0 0.25 0.25 9 721.8 395.5 0.51 0.53
0.066 167 100.00 646.4 609.9 0.26 0.27 6 705.6 613.2 0.40 0.37
0.071 181 100.00 666.7 612.6 0.26 0.27 5 870.6 813.1 0.18 0.20
0.076 180 100.00 675.9 625.6 0.26 0.26 11 690.5 570.2 0.39 0.39
0.081 178 100.00 649.3 607.9 0.25 0.25 14 517.7 559.3 0.40 0.38
0.085 185 100.00 583.8 589.1 0.26 0.25 8 466.1 358.9 0.60 0.52
0.090 194 100.00 548.6 526.8 0.27 0.26 11 730.7 583.2 0.37 0.34
0.095 192 100.00 576.2 564.4 0.25 0.24 12 418.0 403.7 0.48 0.45
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 11. Fom(-acentric, centric, overall v resln:
$GRAPHS:Cycle 11. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0029 13 0.980 33 0.903 46 0.925 0.915
0.0077 30 0.953 40 0.950 70 0.951 0.915
0.0126 41 0.926 39 0.891 80 0.909 0.915
0.0175 56 0.937 37 0.826 93 0.893 0.915
0.0223 64 0.928 38 0.855 102 0.901 0.916
0.0272 81 0.934 48 0.843 129 0.900 0.916
0.0320 73 0.934 39 0.869 112 0.911 0.916
0.0369 86 0.927 39 0.861 125 0.906 0.916
0.0418 100 0.953 41 0.841 141 0.920 0.916
0.0466 109 0.937 39 0.864 148 0.918 0.916
0.0515 113 0.928 46 0.836 159 0.901 0.916
0.0563 114 0.947 45 0.903 159 0.934 0.916
0.0612 122 0.941 36 0.839 158 0.918 0.916
0.0661 124 0.910 43 0.825 167 0.888 0.916
0.0709 141 0.913 40 0.736 181 0.874 0.916
0.0758 133 0.924 47 0.652 180 0.853 0.916
0.0806 140 0.905 38 0.836 178 0.890 0.916
0.0855 145 0.901 40 0.798 185 0.879 0.916
0.0904 152 0.885 42 0.795 194 0.865 0.916
0.0952 151 0.894 41 0.797 192 0.874 0.916
$$
Resolution limits = 46.932 3.200
Number of used reflections = 2799
Percentage observed = 99.8303
Percentage of free reflections = 4.8606
Overall R factor = 0.2741
Free R factor = 0.3856
Overall weighted R factor = 0.2809
Free weighted R factor = 0.3788
Overall correlation coefficient = 0.8143
Free correlation coefficient = 0.6291
DPI based on free R factor = 0.8343
Overall figure of merit = 0.8958
ML based su of positional parameters = 0.6276
ML based su of thermal parameters = 34.2870
-----------------------------------------------------------------------------
Time in seconds: CPU = 5.42
Elapsed = 5.00
**** 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:
$$
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$
$$
0 0.390 0.441 0.884 943.4 0.050 4.403 0.179
1 0.331 0.405 0.889 279.2 0.065 5.299 0.245
2 0.310 0.393 0.892 56.8 0.061 4.758 0.221
3 0.299 0.386 0.893 -85.2 0.062 4.654 0.229
4 0.292 0.386 0.894 -162.9 0.063 4.614 0.238
5 0.287 0.385 0.895 -222.6 0.063 4.574 0.246
6 0.284 0.383 0.895 -255.3 0.062 4.537 0.253
7 0.280 0.385 0.895 -277.0 0.062 4.500 0.258
8 0.278 0.384 0.895 -297.9 0.062 4.462 0.263
9 0.276 0.385 0.896 -329.6 0.061 4.427 0.267
10 0.274 0.386 0.896 -338.8 0.061 4.388 0.271
$$
Refmac_5.3.0037: End of Refmac_5.3.0037 Times: User: 8.1s System: 0.4s Elapsed: 0:09
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
Result:
170 residues were built in 2 chains, the longest having 127 residues. 165 residues were sequenced, after pruning.
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
############################################################### ############################################################### ############################################################### ### CCP4 6.0: cbuccaneer version 1.0.0 : 04/10/07## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:13:36 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.
Copyright 2002-2007 Kevin Cowtan and University of York.
$TEXT:Reference: $$ Please reference $$ 'The Buccaneer software for automated model building' Cowtan K. (2006) Acta Cryst. D62, 1002-1011. $$
title [No title given] pdbin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.mtz colin-ref-fo /*/*/[FP.F_sigF.F,FP.F_sigF.sigF] colin-ref-hl /*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D] seqin-wrk /home/cowtan/test/1vjf.seq mtzin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz colin-wrk-fo /*/*/[FP,SIGFP] colin-wrk-free /*/*/[FreeR_flag] colin-wrk-phifom /*/*/[PHCOMB,FOM] pdbin-wrk /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb pdbout-wrk /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb find grow join link sequence correct filter ncsbuild prune rebuild cycles 1 correlation-mode sequence-reliability 0.95 new-residue-name UNK resolution 2.0 Cycle: 1 C-alphas after finding: 199 C-alphas after growing: 273 C-alphas after joining: 193 C-alphas linked: 0 C-alphas sequenced: 169 C-alphas corrected: 0 C-alphas after filtering: 179 C-alphas after NCS build: 179 C-alphas after pruning: 170 C-alphas after rebuilding: 170
Internal cycle 1 170 residues were built in 2 chains, the longest having 127 residues. 165 residues were sequenced, after pruning.
$TEXT:Result: $$ $$ 170 residues were built in 2 chains, the longest having 127 residues. 165 residues were sequenced, after pruning. $$
cbuccaneer: Normal termination Times: User: 90.1s System: 0.3s Elapsed: 1:31
Current view: summary only [Show full logfile] [Hide logfile]
Current view: full logfile [Show logfile summary] [Hide logfile]
| Initial | After 10 cycles | |
|---|---|---|
| R factor | 0.341 | 0.232 |
| Rfree | 0.411 | 0.355 |
|
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 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. 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 10. Rfactor analysis, F distribution v resln Cycle 10. Fom(<cos(DelPhi)>-acentric, centric, overall v resln Cycle 11. Rfactor analysis, F distribution v resln Cycle 11. 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_5.3.0037 version 5.3.0037 : 03/29/06## ############################################################### User: cowtan Run date: 20/11/2007 Run time: 15:15:07 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--- title [No title given]
TITL
Data line--- weight MATRIX 0.1
WEIG
Data line--- labin HLA=pirate.ABCD.A HLB=pirate.ABCD.B HLC=pirate.ABCD.C HLD=pirate.ABCD.D FREE=FreeR_flag FP=FP SIGFP=SIGFP
LABI
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 PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT
REFI
Data line--- ncyc 10
NCYC
Data line--- scal type SIMP LSSC ANISO EXPE
SCAL
Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
SOLV
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--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
LABO
Data line--- PNAME buccaneer
PNAM
Data line--- DNAME buccaneer
DNAM
Data line--- RSIZE 80
RSIZ
Data line--- END
END
OPENED INPUT MTZ FILE
Logical Name: HKLIN Filename: /home/cowtan/test/1vjf-3.2A.mtz
Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib
**** Input and Default parameters# ****
Input coordinate file. Logical name - XYZIN actual file name - /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
Input reflection file. Logical name - HKLIN actual file name - /home/cowtan/test/1vjf-3.2A.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
Cell from mtz : 50.903 50.903 121.411 90.000 90.000 90.000
Space group from mtz: number - 96; name - P43212
Refinement type : Restrained
**** Makecif parameters ****
Dictionary files for restraints : /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/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 : Phase modified Maximum Likelihood for Fs
Phase Blurred by Scale*Exp(-B s**2) : 1.00 0.00
**** 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 1.400
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 0.0049
Refinement of individual isotropic Bfactors
Refinement resln : 46.9323 3.2002
Estimated number of reflections : 3404
Free R exclusion - flag equals: 0
Weighting by comparison of trace of matrix
Weighting parameters : 0.1000
Refinement cycles : 10
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
Input phases not used in SigmaA estimation
Scaling and SigmaA resln: 46.9323 3.2002
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/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.12
_lib_update 20/09/07
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2436
with complete description : 454
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: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/atomsf.lib
Number of atoms : 1287
Number of residues : 170
Number of chains : 2
I am reading library. Please wait.
mon_lib.cif
WARNING : CIS peptide bond is found, angle = 88.83
ch:BB res: 138 PRO --> 139 VAL
INFO: link is found (not be used) dist= 1.616 ideal_dist= 1.457
ch:AA res: 117 LEU at:CD1 .->ch:AA res: 127 PHE at:CZ .
INFO: link is found (not be used) dist= 1.526 ideal_dist= 1.195
ch:AA res: 137 ASP at:OD1 .->ch:BB res: 138 PRO at:N .
INFO: link is found (not be used) dist= 1.473 ideal_dist= 1.337
ch:AA res: 137 ASP at:OD1 .->ch:BB res: 138 PRO at:CG .
INFO: link is found (not be used) dist= 1.426 ideal_dist= 1.337
ch:AA res: 137 ASP at:OD1 .->ch:BB res: 138 PRO at:CD .
--------------------------------
--- title of input coord file ---
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-XX
--------------------------------
ATTENTION: atom:O ASP 137 AA is missing in the structure
ATTENTION: atom:O UNK 180 BB is missing in the structure
Number of chains : 2
Total number of monomers : 170
Number of atoms : 1289
Number of missing atoms : 2
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0
Number of bonds restraints : 1313
Number of angles restraints : 1777
Number of torsions restraints : 898
Number of chiralities : 207
Number of planar groups : 229
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 2948
Number of reflection read 2948
CGMAT cycle number = 1
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 27 GLY C . - A 28 VAL N . mod.= 0.972 id.= 1.329 dev= 0.357 sig.= 0.014
A 28 VAL C . - A 29 ASP N . mod.= 1.067 id.= 1.329 dev= 0.262 sig.= 0.014
A 29 ASP N . - A 29 ASP CA . mod.= 1.152 id.= 1.458 dev= 0.306 sig.= 0.021
A 30 HIS C . - A 31 LYS N . mod.= 1.043 id.= 1.329 dev= 0.286 sig.= 0.014
A 32 THR CA . - A 32 THR C . mod.= 1.295 id.= 1.525 dev= 0.230 sig.= 0.021
A 36 PRO CD . - A 36 PRO N . mod.= 2.226 id.= 1.473 dev= -0.753 sig.= 0.014
A 37 PRO CD . - A 37 PRO N . mod.= 2.082 id.= 1.473 dev= -0.609 sig.= 0.014
A 52 PRO CD . - A 52 PRO N . mod.= 1.990 id.= 1.473 dev= -0.517 sig.= 0.014
A 105 LEU C . - A 106 GLY N . mod.= 1.176 id.= 1.329 dev= 0.153 sig.= 0.014
A 109 PRO CD . - A 109 PRO N . mod.= 1.790 id.= 1.473 dev= -0.317 sig.= 0.014
B 138 PRO CD . - B 138 PRO N . mod.= 2.059 id.= 1.473 dev= -0.586 sig.= 0.014
B 138 PRO C . - B 139 VAL N . mod.= 1.103 id.= 1.329 dev= 0.226 sig.= 0.014
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 30 HIS O - A 31 LYS N mod.= 91.04 id.= 123.00 dev= 31.965 sig.= 1.600
A 30 HIS CA - A 31 LYS N mod.= 148.06 id.= 116.20 dev=-31.864 sig.= 2.000
A 30 HIS C - A 31 LYS CA mod.= 151.13 id.= 121.70 dev=-29.426 sig.= 1.800
A 32 THR O - A 33 LEU N mod.= 105.57 id.= 123.00 dev= 17.428 sig.= 1.600
A 35 HIS O - A 36 PRO N mod.= 85.16 id.= 123.00 dev= 37.840 sig.= 1.600
A 35 HIS CA - A 36 PRO N mod.= 154.01 id.= 116.90 dev=-37.106 sig.= 1.500
A 36 PRO CA - A 36 PRO CD mod.= 80.63 id.= 112.00 dev= 31.373 sig.= 1.400
A 36 PRO N - A 36 PRO CG mod.= 79.49 id.= 103.20 dev= 23.713 sig.= 1.500
A 37 PRO CA - A 37 PRO CD mod.= 82.94 id.= 112.00 dev= 29.060 sig.= 1.400
A 37 PRO N - A 37 PRO CG mod.= 81.37 id.= 103.20 dev= 21.826 sig.= 1.500
A 52 PRO CA - A 52 PRO CD mod.= 88.49 id.= 112.00 dev= 23.509 sig.= 1.400
A 52 PRO N - A 52 PRO CG mod.= 80.85 id.= 103.20 dev= 22.348 sig.= 1.500
A 105 LEU O - A 106 GLY N mod.= 91.18 id.= 123.00 dev= 31.821 sig.= 1.600
A 105 LEU CA - A 106 GLY N mod.= 147.90 id.= 116.20 dev=-31.705 sig.= 2.000
A 106 GLY C - A 107 VAL CA mod.= 103.57 id.= 121.70 dev= 18.126 sig.= 1.800
A 107 VAL N - A 107 VAL C mod.= 142.13 id.= 111.20 dev=-30.925 sig.= 2.800
A 109 PRO N - A 109 PRO CG mod.= 80.41 id.= 103.20 dev= 22.793 sig.= 1.500
B 138 PRO CA - B 138 PRO CD mod.= 88.71 id.= 112.00 dev= 23.294 sig.= 1.400
B 138 PRO N - B 138 PRO CG mod.= 79.50 id.= 103.20 dev= 23.695 sig.= 1.500
B 138 PRO O - B 139 VAL N mod.= 64.86 id.= 123.00 dev= 58.135 sig.= 1.600
B 138 PRO CA - B 139 VAL N mod.= 174.26 id.= 116.20 dev=-58.064 sig.= 2.000
B 138 PRO C - B 139 VAL CA mod.= 168.43 id.= 121.70 dev=-46.729 sig.= 1.800
**** Torsion angle outliers ****
Torsion angle deviations from the ideal >10.000Sigma will be monitored
A 52 PRO CA - A 53 GLY CA mod.=-123.55 id.= 180.00 per.= 1 dev= -56.45 sig.= 5.00
A 90 SER CA - A 91 GLY CA mod.= -93.24 id.= 180.00 per.= 1 dev= -86.76 sig.= 5.00
B 138 PRO CA - B 139 VAL CA mod.= -88.83 id.= 0.00 per.= 1 dev= 88.83 sig.= 5.00
**** Large deviation of atoms from planarity ****
Deviations from the planarity >10.000Sigma will be monitored
Atom: A 37 PRO N deviation= -0.32 sigma.= 0.02
Atom: A 52 PRO N deviation= -0.33 sigma.= 0.02
Atom: A 109 PRO N deviation= -0.22 sigma.= 0.02
**** VDW outliers ****
VDW deviations from the ideal >10.000Sigma or dist < 1.000 will be monitored
A 32 THR CG2 . - B 150 THR CG2 . mod.= 1.776 id.= 3.880 dev= -2.10 sig.= 0.20 sym.= 1 0 0 0
A 117 LEU CD1 . - A 127 PHE CZ . mod.= 1.616 id.= 3.760 dev= -2.14 sig.= 0.20 sym.= 1 0 0 0
A 137 ASP OD1 . - B 138 PRO CD . mod.= 1.426 id.= 3.440 dev= -2.01 sig.= 0.20 sym.= 1 0 0 0
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.047 0.022
Bond angles : refined atoms 1777 5.127 1.960
Torsion angles, period 1. refined 168 16.126 5.000
Torsion angles, period 2. refined 54 37.237 23.889
Torsion angles, period 3. refined 218 7.072 15.000
Torsion angles, period 4. refined 7 8.813 15.000
Chiral centres: refined atoms 207 0.180 0.200
Planar groups: refined atoms 976 0.020 0.020
VDW repulsions: refined atoms 815 0.502 0.200
VDW; torsion: refined atoms 903 0.363 0.200
HBOND: refined atoms 52 0.359 0.200
VDW repulsions; symmetry: refined atoms 59 0.604 0.200
HBOND; symmetry: refined atoms 4 0.441 0.200
M. chain bond B values: refined atoms 840 0.000 1.500
M. chain angle B values: refined atoms 1342 0.000 2.000
S. chain bond B values: refined atoms 473 0.000 3.000
S. chain angle B values: refined atoms 435 0.000 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.513, B = -44.340
Partial structure 1: scale = 0.331, B = 19.044
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
**** Things for loggraph, R factor and others ****
$TABLE: Cycle 1. Rfactor analysis, F distribution v resln :
$GRAPHS:Cycle 1. 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:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.003 46 96.23 520.9 417.0 0.44 0.50 5 607.2 579.2 0.23 0.29
0.008 70 98.63 775.2 606.5 0.33 0.35 2 454.9 238.8 0.47 0.42
0.013 80 100.00 704.9 626.0 0.25 0.25 9 598.7 471.1 0.42 0.50
0.017 93 100.00 501.7 511.8 0.35 0.34 6 539.4 493.8 0.36 0.40
0.022 102 100.00 484.5 494.7 0.37 0.37 4 664.8 502.7 0.58 0.52
0.027 129 100.00 503.9 482.5 0.39 0.39 2 778.9 488.3 0.40 0.37
0.032 112 98.41 499.3 509.9 0.41 0.40 12 565.2 454.9 0.37 0.34
0.037 125 100.00 639.2 624.2 0.37 0.38 9 680.4 696.5 0.44 0.44
0.042 141 100.00 706.0 706.4 0.29 0.31 5 811.1 613.8 0.31 0.30
0.047 148 100.00 684.6 635.8 0.33 0.34 3 624.0 371.4 0.52 0.44
0.051 159 100.00 686.7 618.5 0.33 0.34 6 831.4 695.0 0.24 0.25
0.056 159 100.00 775.3 677.8 0.31 0.32 4 608.0 516.7 0.50 0.48
0.061 158 100.00 693.1 616.5 0.31 0.31 9 686.3 424.7 0.47 0.42
0.066 167 100.00 614.6 570.8 0.34 0.35 6 670.9 343.4 0.61 0.58
0.071 181 100.00 633.9 553.3 0.32 0.33 5 827.9 622.9 0.35 0.37
0.076 180 100.00 642.7 592.8 0.37 0.36 11 656.6 557.5 0.37 0.37
0.081 178 100.00 617.4 579.4 0.32 0.32 14 492.3 472.1 0.43 0.36
0.085 185 100.00 555.1 521.2 0.36 0.34 8 443.2 294.6 0.41 0.38
0.090 194 100.00 521.7 484.0 0.34 0.34 11 694.8 453.9 0.41 0.37
0.095 192 100.00 547.9 516.6 0.40 0.40 12 397.5 362.9 0.48 0.45
$$
**** 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:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0029 13 0.980 33 0.908 46 0.929 0.913
0.0077 30 0.949 40 0.943 70 0.946 0.910
0.0126 41 0.928 39 0.878 80 0.903 0.908
0.0175 56 0.935 37 0.829 93 0.893 0.907
0.0223 64 0.925 38 0.861 102 0.901 0.905
0.0272 81 0.925 48 0.817 129 0.885 0.904
0.0320 73 0.922 39 0.865 112 0.902 0.902
0.0369 86 0.924 39 0.851 125 0.901 0.901
0.0418 100 0.948 41 0.847 141 0.919 0.900
0.0466 109 0.931 39 0.847 148 0.909 0.899
0.0515 113 0.923 46 0.824 159 0.894 0.898
0.0563 114 0.935 45 0.901 159 0.925 0.898
0.0612 122 0.935 36 0.821 158 0.909 0.897
0.0661 124 0.895 43 0.802 167 0.871 0.896
0.0709 141 0.892 40 0.712 181 0.852 0.895
0.0758 133 0.903 47 0.632 180 0.833 0.894
0.0806 140 0.896 38 0.796 178 0.875 0.894
0.0855 145 0.891 40 0.741 185 0.859 0.893
0.0904 152 0.872 42 0.748 194 0.845 0.892
0.0952 151 0.878 41 0.809 192 0.864 0.891
$$
Resolution limits = 46.932 3.200
Number of used reflections = 2799
Percentage observed = 99.8303
Percentage of free reflections = 4.8606
Overall R factor = 0.3414
Free R factor = 0.4106
Overall weighted R factor = 0.3456
Free weighted R factor = 0.3986
Overall correlation coefficient = 0.7216
Free correlation coefficient = 0.5801
DPI based on free R factor = 0.9064
Overall figure of merit = 0.8842
ML based su of positional parameters = 0.8066
ML based su of thermal parameters = 44.9462
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 2
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.054 0.022
Bond angles : refined atoms 1777 4.728 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.519, B = -8.761
Partial structure 1: scale = 0.327, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2820
Free R factor = 0.3768
Overall figure of merit = 0.8916
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 3
weigth matrix 9.9999994E-02
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.053 0.022
Bond angles : refined atoms 1777 4.533 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.522, B = -8.257
Partial structure 1: scale = 0.327, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2626
Free R factor = 0.3852
Overall figure of merit = 0.8902
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 4
weigth matrix 9.9999994E-02
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.056 0.022
Bond angles : refined atoms 1777 4.445 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.527, B = -7.481
Partial structure 1: scale = 0.325, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2555
Free R factor = 0.3855
Overall figure of merit = 0.8932
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 5
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.056 0.022
Bond angles : refined atoms 1777 4.208 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.526, B = -8.132
Partial structure 1: scale = 0.326, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2492
Free R factor = 0.3836
Overall figure of merit = 0.8922
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 6
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.057 0.022
Bond angles : refined atoms 1777 4.263 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.530, B = -7.742
Partial structure 1: scale = 0.324, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2444
Free R factor = 0.3721
Overall figure of merit = 0.8947
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 7
weigth matrix 9.9999994E-02
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.057 0.022
Bond angles : refined atoms 1777 4.136 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.530, B = -7.880
Partial structure 1: scale = 0.326, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2413
Free R factor = 0.3740
Overall figure of merit = 0.8937
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 8
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.056 0.022
Bond angles : refined atoms 1777 4.096 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.534, B = -7.419
Partial structure 1: scale = 0.326, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2382
Free R factor = 0.3597
Overall figure of merit = 0.8966
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 9
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.056 0.022
Bond angles : refined atoms 1777 4.084 1.960
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.535, B = -7.289
Partial structure 1: scale = 0.327, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall R factor = 0.2361
Free R factor = 0.3670
Overall figure of merit = 0.8956
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
CGMAT cycle number = 10
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 127 PHE CE1 . - A 127 PHE CZ . mod.= 1.775 id.= 1.382 dev= -0.393 sig.= 0.030
A 137 ASP CG . - A 137 ASP OD2 . mod.= 1.574 id.= 1.249 dev= -0.325 sig.= 0.019
A 137 ASP CA . - A 137 ASP C . mod.= 1.797 id.= 1.525 dev= -0.272 sig.= 0.021
B 145 LYS CD . - B 145 LYS CE . mod.= 1.823 id.= 1.520 dev= -0.303 sig.= 0.030
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 106 GLY C - A 107 VAL CA mod.= 102.00 id.= 121.70 dev= 19.700 sig.= 1.800
A 107 VAL N - A 107 VAL C mod.= 141.34 id.= 111.20 dev=-30.136 sig.= 2.800
**** Torsion angle outliers ****
Torsion angle deviations from the ideal >10.000Sigma will be monitored
A 52 PRO CA - A 53 GLY CA mod.=-126.82 id.= 180.00 per.= 1 dev= -53.18 sig.= 5.00
A 90 SER CA - A 91 GLY CA mod.= -85.37 id.= 180.00 per.= 1 dev= -94.63 sig.= 5.00
B 138 PRO CA - B 139 VAL CA mod.=-117.43 id.= 0.00 per.= 1 dev= 117.43 sig.= 5.00
weigth matrix 0.1000000
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.054 0.022
Bond angles : refined atoms 1777 3.980 1.960
Torsion angles, period 1. refined 168 16.818 5.000
Torsion angles, period 2. refined 54 39.210 23.889
Torsion angles, period 3. refined 218 23.373 15.000
Torsion angles, period 4. refined 7 24.130 15.000
Chiral centres: refined atoms 207 0.227 0.200
Planar groups: refined atoms 976 0.012 0.020
VDW repulsions: refined atoms 657 0.341 0.200
VDW; torsion: refined atoms 888 0.379 0.200
HBOND: refined atoms 47 0.333 0.200
VDW repulsions; symmetry: refined atoms 38 0.387 0.200
HBOND; symmetry: refined atoms 1 0.188 0.200
M. chain bond B values: refined atoms 870 0.466 1.500
M. chain angle B values: refined atoms 1342 0.601 2.000
S. chain bond B values: refined atoms 501 2.367 3.000
S. chain angle B values: refined atoms 435 3.326 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.537, B = -7.030
Partial structure 1: scale = 0.326, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
**** Things for loggraph, R factor and others ****
$TABLE: Cycle 10. Rfactor analysis, F distribution v resln :
$GRAPHS:Cycle 10. v. resln :N:1,6,7,11,12:
:Cycle 10. and v. resln :N:1,4,5,9,10:
:Cycle 10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.003 46 96.23 497.7 415.7 0.39 0.43 5 580.1 461.8 0.34 0.41
0.008 70 98.63 740.7 656.9 0.22 0.24 2 434.6 232.5 0.46 0.40
0.013 80 100.00 673.5 617.6 0.22 0.23 9 572.0 461.5 0.33 0.41
0.017 93 100.00 479.4 488.9 0.31 0.31 6 515.4 524.3 0.37 0.36
0.022 102 100.00 462.9 475.3 0.29 0.30 4 635.1 468.6 0.55 0.52
0.027 129 100.00 481.4 475.1 0.33 0.33 2 744.1 609.6 0.18 0.24
0.032 112 98.41 477.0 490.4 0.29 0.29 12 540.0 432.4 0.33 0.30
0.037 125 100.00 610.7 624.6 0.26 0.27 9 650.1 657.4 0.38 0.35
0.042 141 100.00 674.5 671.3 0.19 0.20 5 774.9 595.5 0.23 0.24
0.047 148 100.00 654.0 632.2 0.22 0.23 3 596.1 447.6 0.25 0.18
0.051 159 100.00 656.1 633.8 0.19 0.19 6 794.3 709.9 0.22 0.23
0.056 159 100.00 740.8 694.8 0.20 0.20 4 580.9 603.9 0.39 0.38
0.061 158 100.00 662.2 598.7 0.23 0.24 9 655.7 466.7 0.36 0.38
0.066 167 100.00 587.2 543.2 0.24 0.24 6 641.0 462.7 0.33 0.35
0.071 181 100.00 605.6 558.4 0.22 0.23 5 790.9 825.0 0.37 0.40
0.076 180 100.00 614.0 594.8 0.24 0.24 11 627.3 640.0 0.32 0.29
0.081 178 100.00 589.9 554.9 0.21 0.22 14 470.3 462.2 0.31 0.29
0.085 185 100.00 530.3 520.1 0.23 0.23 8 423.4 406.9 0.58 0.47
0.090 194 100.00 498.4 471.1 0.24 0.23 11 663.8 516.5 0.42 0.39
0.095 192 100.00 523.4 504.1 0.23 0.23 12 379.7 285.4 0.45 0.41
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 10. Fom(-acentric, centric, overall v resln:
$GRAPHS:Cycle 10. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0029 13 0.981 33 0.945 46 0.955 0.939
0.0077 30 0.953 40 0.960 70 0.957 0.934
0.0126 41 0.931 39 0.898 80 0.915 0.931
0.0175 56 0.942 37 0.829 93 0.897 0.929
0.0223 64 0.926 38 0.863 102 0.902 0.927
0.0272 81 0.937 48 0.823 129 0.895 0.925
0.0320 73 0.935 39 0.872 112 0.913 0.923
0.0369 86 0.930 39 0.854 125 0.907 0.921
0.0418 100 0.953 41 0.852 141 0.923 0.920
0.0466 109 0.938 39 0.860 148 0.918 0.918
0.0515 113 0.929 46 0.839 159 0.903 0.917
0.0563 114 0.951 45 0.918 159 0.941 0.915
0.0612 122 0.942 36 0.836 158 0.918 0.914
0.0661 124 0.911 43 0.808 167 0.885 0.913
0.0709 141 0.909 40 0.739 181 0.872 0.912
0.0758 133 0.920 47 0.633 180 0.845 0.911
0.0806 140 0.905 38 0.845 178 0.892 0.910
0.0855 145 0.904 40 0.790 185 0.879 0.908
0.0904 152 0.890 42 0.795 194 0.869 0.907
0.0952 151 0.897 41 0.828 192 0.882 0.906
$$
Resolution limits = 46.932 3.200
Number of used reflections = 2799
Percentage observed = 99.8303
Percentage of free reflections = 4.8606
Overall R factor = 0.2345
Free R factor = 0.3561
Overall weighted R factor = 0.2409
Free weighted R factor = 0.3519
Overall correlation coefficient = 0.8691
Free correlation coefficient = 0.6979
DPI based on free R factor = 0.7862
Overall figure of merit = 0.8974
ML based su of positional parameters = 0.6422
ML based su of thermal parameters = 35.9339
-----------------------------------------------------------------------------
Trying gamma equal 0.0000000E+00
Convergence reached with no gamma cycles
**** Bond distance outliers ****
Bond distance deviations from the ideal >10.000Sigma will be monitored
A 90 SER CB . - A 90 SER OG . mod.= 1.630 id.= 1.417 dev= -0.213 sig.= 0.020
A 101 MET SD . - A 101 MET CE . mod.= 1.538 id.= 1.791 dev= 0.253 sig.= 0.025
A 127 PHE CE1 . - A 127 PHE CZ . mod.= 1.914 id.= 1.382 dev= -0.532 sig.= 0.030
A 137 ASP CG . - A 137 ASP OD2 . mod.= 1.447 id.= 1.249 dev= -0.198 sig.= 0.019
B 145 LYS CD . - B 145 LYS CE . mod.= 1.826 id.= 1.520 dev= -0.306 sig.= 0.030
**** Bond angle outliers ****
Bond angle deviations from the ideal >10.000Sigma will be monitored
A 106 GLY C - A 107 VAL CA mod.= 102.27 id.= 121.70 dev= 19.431 sig.= 1.800
A 107 VAL N - A 107 VAL C mod.= 140.82 id.= 111.20 dev=-29.618 sig.= 2.800
A 137 ASP N - A 137 ASP C mod.= 139.88 id.= 111.20 dev=-28.678 sig.= 2.800
**** Torsion angle outliers ****
Torsion angle deviations from the ideal >10.000Sigma will be monitored
A 52 PRO CA - A 53 GLY CA mod.=-127.35 id.= 180.00 per.= 1 dev= -52.65 sig.= 5.00
A 53 GLY CA - A 54 GLY CA mod.=-127.44 id.= 180.00 per.= 1 dev= -52.56 sig.= 5.00
A 90 SER CA - A 91 GLY CA mod.= -92.61 id.= 180.00 per.= 1 dev= -87.39 sig.= 5.00
B 138 PRO CA - B 139 VAL CA mod.=-113.87 id.= 0.00 per.= 1 dev= 113.87 sig.= 5.00
WRITTEN OUTPUT MTZ FILE
Logical Name: HKLOUT Filename: /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
-------------------------------------------------------------------------------
Restraint type N restraints Rms Delta Av(Sigma)
Bond distances: refined atoms 1313 0.054 0.022
Bond angles : refined atoms 1777 3.918 1.960
Torsion angles, period 1. refined 168 16.352 5.000
Torsion angles, period 2. refined 54 39.244 23.889
Torsion angles, period 3. refined 218 23.553 15.000
Torsion angles, period 4. refined 7 24.443 15.000
Chiral centres: refined atoms 207 0.228 0.200
Planar groups: refined atoms 976 0.012 0.020
VDW repulsions: refined atoms 649 0.338 0.200
VDW; torsion: refined atoms 896 0.375 0.200
HBOND: refined atoms 48 0.330 0.200
VDW repulsions; symmetry: refined atoms 38 0.312 0.200
M. chain bond B values: refined atoms 873 0.476 1.500
M. chain angle B values: refined atoms 1342 0.627 2.000
S. chain bond B values: refined atoms 501 2.370 3.000
S. chain angle B values: refined atoms 435 3.313 4.500
-------------------------------------------------------------------------------
-----------------------------------------------------------------------------
Overall : scale = 0.537, B = -7.199
Partial structure 1: scale = 0.329, B = -10.000
Overall anisotropic scale factors
B11 = 0.00 B22 = 0.00 B33 = 0.00 B12 = 0.00 B13 = 0.00 B23 = 0.00
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
**** Things for loggraph, R factor and others ****
$TABLE: Cycle 11. Rfactor analysis, F distribution v resln :
$GRAPHS:Cycle 11. v. resln :N:1,6,7,11,12:
:Cycle 11. and v. resln :N:1,4,5,9,10:
:Cycle 11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free WR_free $$
$$
0.003 46 96.23 497.4 404.9 0.39 0.44 5 579.7 461.5 0.34 0.41
0.008 70 98.63 740.2 655.3 0.21 0.23 2 434.3 237.5 0.45 0.40
0.013 80 100.00 673.1 619.6 0.21 0.22 9 571.6 453.9 0.33 0.41
0.017 93 100.00 479.0 488.2 0.31 0.31 6 515.0 543.2 0.40 0.38
0.022 102 100.00 462.6 474.1 0.29 0.30 4 634.7 463.8 0.54 0.51
0.027 129 100.00 481.1 472.4 0.32 0.32 2 743.6 622.3 0.16 0.21
0.032 112 98.41 476.7 490.4 0.29 0.29 12 539.6 430.8 0.33 0.31
0.037 125 100.00 610.3 626.4 0.25 0.26 9 649.7 671.7 0.37 0.34
0.042 141 100.00 674.1 672.2 0.19 0.20 5 774.4 595.9 0.23 0.24
0.047 148 100.00 653.6 629.8 0.22 0.22 3 595.8 479.1 0.20 0.11
0.051 159 100.00 655.7 635.3 0.19 0.19 6 793.8 710.7 0.22 0.22
0.056 159 100.00 740.3 694.8 0.19 0.20 4 580.5 611.5 0.39 0.37
0.061 158 100.00 661.8 601.3 0.23 0.23 9 655.3 464.5 0.35 0.36
0.066 167 100.00 586.8 545.2 0.23 0.23 6 640.5 454.7 0.34 0.37
0.071 181 100.00 605.2 562.4 0.22 0.22 5 790.4 812.9 0.37 0.40
0.076 180 100.00 613.6 594.0 0.23 0.23 11 626.9 643.7 0.35 0.32
0.081 178 100.00 589.5 560.3 0.21 0.22 14 470.0 463.6 0.28 0.26
0.085 185 100.00 530.0 525.0 0.23 0.23 8 423.1 399.3 0.62 0.50
0.090 194 100.00 498.1 470.1 0.23 0.22 11 663.4 513.3 0.43 0.40
0.095 192 100.00 523.1 509.5 0.23 0.22 12 379.5 298.8 0.42 0.38
$$
**** Fom and SigmaA vs resolution ****
$TABLE: Cycle 11. Fom(-acentric, centric, overall v resln:
$GRAPHS:Cycle 11. M(Fom) v. resln :N:1,3,5,7,8:
$$
<4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 $$
$$
0.0029 13 0.982 33 0.944 46 0.954 0.939
0.0077 30 0.954 40 0.959 70 0.957 0.935
0.0126 41 0.931 39 0.896 80 0.914 0.931
0.0175 56 0.942 37 0.829 93 0.897 0.928
0.0223 64 0.926 38 0.864 102 0.903 0.926
0.0272 81 0.938 48 0.820 129 0.894 0.924
0.0320 73 0.934 39 0.871 112 0.912 0.922
0.0369 86 0.930 39 0.853 125 0.906 0.920
0.0418 100 0.953 41 0.849 141 0.922 0.918
0.0466 109 0.938 39 0.856 148 0.916 0.917
0.0515 113 0.930 46 0.840 159 0.904 0.915
0.0563 114 0.950 45 0.916 159 0.940 0.913
0.0612 122 0.943 36 0.838 158 0.919 0.912
0.0661 124 0.911 43 0.808 167 0.885 0.911
0.0709 141 0.909 40 0.732 181 0.870 0.909
0.0758 133 0.919 47 0.640 180 0.846 0.908
0.0806 140 0.904 38 0.849 178 0.892 0.907
0.0855 145 0.904 40 0.785 185 0.878 0.906
0.0904 152 0.888 42 0.792 194 0.867 0.905
0.0952 151 0.896 41 0.829 192 0.882 0.903
$$
Resolution limits = 46.932 3.200
Number of used reflections = 2799
Percentage observed = 99.8303
Percentage of free reflections = 4.8606
Overall R factor = 0.2317
Free R factor = 0.3549
Overall weighted R factor = 0.2377
Free weighted R factor = 0.3510
Overall correlation coefficient = 0.8723
Free correlation coefficient = 0.6974
DPI based on free R factor = 0.7835
Overall figure of merit = 0.8970
ML based su of positional parameters = 0.6422
ML based su of thermal parameters = 35.9339
-----------------------------------------------------------------------------
Time in seconds: CPU = 5.98
Elapsed = 6.00
**** 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:
$$
Ncyc Rfact Rfree FOM LLG rmsBOND rmsANGLE rmsCHIRAL $$
$$
0 0.341 0.411 0.884 282.3 0.047 5.127 0.180
1 0.282 0.377 0.892 -418.1 0.054 4.728 0.201
2 0.263 0.385 0.890 -521.1 0.053 4.533 0.221
3 0.256 0.386 0.893 -696.1 0.056 4.445 0.239
4 0.249 0.384 0.892 -690.9 0.056 4.208 0.238
5 0.244 0.372 0.895 -805.9 0.057 4.263 0.240
6 0.241 0.374 0.894 -792.9 0.057 4.136 0.238
7 0.238 0.360 0.897 -934.5 0.056 4.096 0.233
8 0.236 0.367 0.896 -924.5 0.056 4.084 0.232
9 0.234 0.356 0.897 -1025.6 0.054 3.980 0.227
10 0.232 0.355 0.897 -1031.4 0.054 3.918 0.228
$$
Refmac_5.3.0037: End of Refmac_5.3.0037 Times: User: 8.9s System: 0.4s Elapsed: 0:09
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Generated for you by baubles 0.0.5 on Thu Dec 20 15:55:15 2007