Please reference use of the software as:
Version: 2.11.1 for linux-ifort made on Feb 1 2011 at 02:02:52
Licenced to: Global Phasing - temporary key
Today is Tue Feb 8 10:03:43 2011
Software will expire soon : Mon Feb 14 13:27:27 2011
Parsing of the BUSTER cardfile
TITLE : autoBUSTER refinement Cell information (explanation) H lattice: BUSTER assumes hexagonal axes in obverse setting Please make sure that indexing complies with this convention Symmetry information (explanation) Using CCP4 X-ray form factors. Missing structure chemical composition (explanation) Using ATOM block for chemical composition. Shell informationParsing of the TNT cardfile
Reading observations file
List of rejected reflexions (explanation) Number of reflexions in input: 26994 Number of accepted reflexions: 26956 Number of rejected reflexions: 38 Reflexions in test set: 1352 (explanation) Reflexions in working set: 25604 (explanation)
1. Generating initial model
2.10 * Shannon sampling rate. NX NY NZ: 288 288 180 Effective Shannon rates are: 2.32 2.32 2.65 Allocated BUFFER of size: 57.349 Mb. Initial Geometry Information (explanation) No missing atoms declared Summary of model volumes (explanation) No missing atoms declared: no prior computed Computing bulk solvent model scattering NCSMASK PDB radius for solvent mask: 2.15 Angstrom running PDBSET (setting cell and spacegroup P1) ... done running NCSMASK [1] (creating mask, SMOOTH 1.20779) ... done running MAPDUMP (to check if reduction to unit cell is needed) ... done running MAPMASK (converting mask to map) ... done Generation of babslv by theta-filter (explanation) Electron density in frg mask: 0.420 Å-1 (explanation) FOBS put on rough absolute scale by Wilson plot : K = 0.18822E+01 B = -26.452 Setting starting scale K to value from Wilson scaling: 1.88218 Setting starting scale B to value from Wilson scaling: -26.45212Cycle 001: MaxLik scaling and refinement
MaxLik Scaling Cycle 001 (explanation) Wilson plot Statistics in resolution bins just after scaling (explanation) :
<Log-Likelihood> of null-hypothesis (explanation)Structure Factor Amplitudes (explanation) Average Figure of Merit (explanation) Switching off refinement of overall temperature factor Added B = 0.3587 Å2 to all atoms in fragment Added B = 0.3587 Å2 to B_SOLV
gelly refinement module Developed by O. S. Smart, C. Flensburg, W. Paciorek, C. Vonrhein, M. Brandl, T. O. Womack and G. Bricogne Copyright © 2006, 2007 Global Phasing Ltd. All rights reserved. gelly module compilation date Feb 01 2011 02:00:01 gelly uses routines from TNT geometry. References: Tronrud, D. E., Ten Eyck, L. F., Matthews, B. W. (1987) "An Efficient General-Purpose Least-Squares Refinement Program for Macromolecular Structures". Acta Crystallogr A, 43:489-501. Tronrud, D. E. (1997). "The TNT Refinement Package", in Macromolecular Crystallography, Part B, Eds Charlie Carter and Robert Sweet, Methods in Enzymology, 277:306-319. wildcard matching function by Julian Robichaux http://www.nsftools.com Have -type card that specifies calculation type 'one' Control flags set to: -type one \ -screen 100 \ -screen_sigma 3.0 Setting up tnt routines including license check: TNT Stereochemistry Program Version: 5.23.1.0 Licence for Global Phasing - temporary key will soon expire Expiration date: Mon Feb 14 13:27:27 2011 Using TNT geometry routines to load the tnt control file: gelly.tnt Using TNT routines to load initial coordinates from file fragment.cor Have copied information for 4551 atoms from TNT to gelly's store Have some non-(C,N,O,P,S,H,Se) atom types - listed below. You may want to check that the charge states are correct. To correct edit the input pdb adding the charge to columns 79 and 80 of the HETATM record (after element type). For example a chloride ion is set HETATM 4798 CL CL 1015 21.068 14.855 66.797 1.00 13.97 CL-1 A|940:CL1 (CPB) type: CL The TNT WEIGHT cards used this run: -----WEIGHT BOND 2.0 -----WEIGHT ANGLE 2.0 -----WEIGHT IMPROPER 0.0 -----WEIGHT TORSION 2.0 -----WEIGHT PSEUDO 0.0 -----WEIGHT TRIGONAL 2.0 -----WEIGHT PLANE 5.0 -----WEIGHT CONTACT 5.0 -----WEIGHT BCORREL 20.0 -----WEIGHT CHIRAL 5.0 -----WEIGHT NCS 50.0 -----WEIGHT IDEAL 4.0 -----WEIGHT RFACTOR 4 Dictionary versions picked up from NOTE BUSTER_RESTRAINT_DICT cards as: ------ protgeo_eh99.dat (V1.8) 20110121 STANDARD AMINO ACID DICTIONARY. BONDS AND ANGLES FROM ENGH AND HUBER EH99. OTHER VALUES BASED ON PREVIOUS TNT OR TAKEN FROM CCP4. INCLUDES HYDROGEN ATOMS. ------ exoticaa.dat (V1.8) 20100430 COLLECTION OF NON-STANDARD AMINO ACIDS, MAINLY EH91 WITHOUT IDEAL DISTANCE INFO ------ nuclgeo.dat (V1.14) 20091104 ------ bcorrel.dat (V1.15) 20080423 ------ contact.dat (V1.20) 20101123 ------ idealdist_contact.dat (V1.7) 20110119 IDEAL-DISTANCE CONTACT TERM DATA AS USED IN PROLSQ. VALUES USED HERE ARE BASED ON THE REFMAC 5.5 IMPLEMENTATION. ------ restraints CPB by PDB2TNT2.5.9 from coordinates NOTE BUSTER_RESTRAINT_INFO Command: PDB2TNT -i /tmp/scifinder-1297159395-ab_pdb2tnt__32757.pdb -n CPB ------ assume.dat (V1.10) 20110113 Have picked up spacegroup name for pdb output as 'H 3 ' Setting up Chain/Residue arrays Setting up BUSTER_SET groups No NOTE BUSTER_SET type cards found - just produce automatic definitions Now silently applying automatic/dictionary set definitions. For a verbose listing use '-verbose_set' flag. Have defined 12 sets: set: 'All' has 4551 atoms in 577 residues - automatically defined set: 'Empty' has 0 atoms in 0 residues - automatically defined set: 'ExoticAA' has 11 atoms in 1 residues - defined by dictionary file set: 'NotHET' has 4476 atoms in 551 residues - automatically defined set: 'Chain_A' has 2480 atoms in 315 residues - automatically defined set: 'Chain_B' has 2071 atoms in 262 residues - automatically defined set: 'Water' has 20 atoms in 20 residues - defined by dictionary file set: 'StdProtein' has 4477 atoms in 552 residues - defined by dictionary file set: 'Protein' has 4488 atoms in 553 residues - defined by dictionary file set: 'Back' has 2209 atoms in 553 residues - defined by dictionary file set: 'Side' has 2279 atoms in 530 residues - defined by dictionary file set: 'Other' has 43 atoms in 4 residues - defined by dictionary file Interpreting CONSTANT cards: =====CONSTANT OCC Have found and interpreted 1 CONSTANT cards in the TNT input. Before any COMBINE - Number of atoms with fixed xyz = 0 Before any COMBINE - Number of atoms with fixed B = 0 Before any COMBINE - Number of atoms with fixed OCC = 4551 Before any COMBINE - Number of atoms with fixed BIJ = 4551 cf total number of atoms = 4551 There are no COMBINE cards to be found in the TNT card input There are no NOTE BUSTER_COMBINE_RES cards to be found in the TNT card input RANGE allowed for B variables in refinement: from 3.00000 to 300.00000 No 'NOTE BUSTER_TARGET' cards or -target?? args found (used to read coordinates files for soft ncs to external) No 'NOTE BUSTER_OCCSUM' cards found - so not using sum of occupancy restraints No 'NOTE BUSTER_DISTANCE' cards found - so not setting up any additional atom-atom distance restraints No 'NOTE BUSTER_UTILANGLE' cards found - so not setting up any additional restraints on any angle No 'NOTE BUSTER_UTILTOR' cards found - so not setting up any additional sinusoidal restraints on torsions No 'NOTE BUSTER_SIM_DEFINE' cards found - so no similarity restraints will be used No 'NOTE BUSTER_TLS_SET' cards found - so no TLS constraints will be used Number of parameters to describe molecular conformation = 18204 Number of free parameters to be adjusted in refinement = 18204 No command line argument '-tnt_fn' so will use gelly to do geometry function calculations Getting symmetry operators from TNT. gelly will classify symmetry using pdb-like convention: SYMOP SYMMETRY NNNMMM OPERATOR 1555 X,Y,Z 2555 -Y,X-Y,Z 3555 -X+Y,-X,Z 4555 2/3+X,1/3+Y,1/3+Z 5555 2/3-Y,1/3+X-Y,1/3+Z 6555 2/3-X+Y,1/3-X,1/3+Z 7555 1/3+X,2/3+Y,2/3+Z 8555 1/3-Y,2/3+X-Y,2/3+Z 9555 1/3-X+Y,2/3-X,2/3+Z where NNN -> operator number and MMM -> translation vector Ideal-distance contact term setup: Restraint function constants (normally values got from NOTE BUSTER_IDEAL_CONTACT_* cards) Sigma for general contacts 0.200 Angs Sigma for 1-4 contacts 0.200 Angs (contacts across a torsion) Sigma for HBOND pairs 0.200 Angs (contacts between HB_types A and D or B's) Contact distance increment for each atom in HBOND -0.150 Angs ContactD for H-bond acceptor to Hydrogen=vdwAccept+ 0.100 Angs Contact distance increment for 1-4 with an O atom -0.100 Angs Contact distance increment for 1-4 with an N atom -0.100 Angs Contact distance increment for 1-4 with an C atom -0.150 Angs Contact distance increment for 1-4 with any other atom -0.150 Angs Have no dictionary entry giving ccp4 atom types for residue types: TPO CPB will use default ccp4 atom types CUNK NUNK OUNK PUNK SUNK .... where possible. All atoms matched for ccp4 atom type - so ideal contact will be used for all contacts (rather than TNT short). Number of ccp4 atom types used is 29 (H-bound and not H-bound counted separately) Using gelly special position handling. (For TNT instead rerun with argument '-special_tnt') TERM weight number TNT_fn Gelly_fn diff BOND 2.000 4633 1121.379 1121.379 0.000 ANGL 2.000 6291 4684.103 4684.103 0.000 IMPR 0.000 0 0.000 0.000 0.000 TORS 2.000 1609 2200.905 2200.906 0.000 TRIG 2.000 125 4.717 4.717 0.000 PLAN 5.000 649 5241.355 5241.355 0.000 CONT 5.000 0 45.757 0.000 45.757 BCOR 20.000 4633 124076.588 124076.588 0.000 Switching torsion functionial form to sinusoidal rather than split harmonic functional. if you want this not to happen then rerun with '-torsharm' Weight for sinusoidal torsion= 2.000 Checking for bonds that do not have a bcorrel restraint defined No -bcorrel_missing_sigma found. So will set sigma to 10.0 Ang**2 for any bond with no existing bcorrel All bonds have a corresponding bcorrel - so no new added A total of 0 planes have been deactivated because they are duplicated hydrogen-free and with-hydrogen forms. Torsion angles split into peptide omega and other Number of peptide omega angles is 547 Number of other torsion is 1062 Peptide omega angles are monitored rather than directly restrained (PLANE used instead). Now apply the fix to get correct restraints for cis PRO residues Have got 4 bonds records and 8 angles from GEOMETRY cards for the special PROC residue Apply the fix to cis PRO residue A|319 because omega torsion A|318:CA(ASP)=A|318:C(ASP)=A|319:N(PRO)=A|319:CA(PRO) is -2.83 degrees Fix up bond A|319:CA=CB (PRO) ideal from 1.531 to 1.533 actual= 1.537, sigma from 0.020 to 0.018 Angs Fix up bond A|319:CB=CG (PRO) ideal from 1.495 to 1.506 actual= 1.513, sigma from 0.050 to 0.039 Angs Fix up bond A|319:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.491, sigma from 0.033 to 0.027 Angs Fix up bond A|319:CD=N (PRO) ideal from 1.474 to 1.474 actual= 1.472, sigma from 0.014 to 0.014 Angs Fix up angle A|318:C(ASP)=A|319:N(PRO)=A|319:CA(PRO) ideal from 119.3 to 127.0 actual= 125.6, sigma from 1.5 to 2.4 Degs Fix up angle A|318:C(ASP)=A|319:N(PRO)=A|319:CD(PRO) ideal from 128.4 to 120.6 actual= 122.2, sigma from 2.1 to 2.2 Degs Fix up angle A|319:N=CA=CB (PRO) ideal from 103.3 to 102.6 actual= 103.5, sigma from 1.2 to 1.1 Degs Fix up angle A|319:CB=CA=C (PRO) ideal from 111.7 to 112.0 actual= 109.3, sigma from 2.1 to 2.5 Degs Fix up angle A|319:CA=CB=CG (PRO) ideal from 104.8 to 104.0 actual= 106.0, sigma from 1.9 to 1.9 Degs Fix up angle A|319:CB=CG=CD (PRO) ideal from 106.5 to 105.4 actual= 106.1, sigma from 3.9 to 2.3 Degs Fix up angle A|319:CG=CD=N (PRO) ideal from 103.2 to 103.8 actual= 102.7, sigma from 1.5 to 1.2 Degs Fix up angle A|319:CA=N=CD (PRO) ideal from 111.7 to 111.5 actual= 112.2, sigma from 1.4 to 1.4 Degs Weight for ideal-distance contact term= 4.000 No ligand-(fixed protein) contact term will be used MaxLik Scaling Cycle 0002 (explanation) Initial functional value = 6.970916E+05 rms gradient= 652.346 X-ray contribution to function value = 5.126957E+05 Geometry contribution (inc ncs) = 1.843959E+05 Geometry function summary term number weight rms GooF function fn/numb ================================================================================================ BOND bond lengths (angs) 4633 2.000 0.0070 0.348 1122.11 0.242 ANGL bond angles (degs) 6291 2.000 0.99 0.607 4637.98 0.737 TORS split-harmonic tors 1062 0.000 15.86 1.018 0.00 0.000 SINTOR sinusoidal tors 1062 2.000 15.86 1785.29 1.681 TRIG.onal planes (angs) 125 2.000 0.0027 0.137 4.72 0.038 PLAN general plane (angs) 649 5.000 0.0254 1.271 5241.36 8.076 BCORrelations (angs*2) 4633 20.000 6.814 1.157 124076.59 26.781 CONT (bad contacts) 0 5.000 0.00 IDEAL(ideal-dist contact) 5154 4.000 45579.44 CHIRAL (gelly semiharmon) 593 5.000 1948.42 SIM similarity restraint for NCS and/or TARGET 0.00 as none defined OCCSUM restraint on sum of occupanies 0.00 as none defined DISTAN utility restraints interatomic distance 0.00 as none defined UTILANGLE utility angle restraints 0.00 as none defined UTILTOR utility restraints on torsion angles 0.00 as none defined Peptide omega torsion angles 4.86 degs - monitor only WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: WARNING: 2 planes. Worst is 6.5 sigs 0.13 Angs A|176:C=A|176:CA=A|176:O=A|177:N=A|177:CA WARNING: 12 Bcorrel. Worst is 27.2 sigs 120.14 Angs**2 B|48:SD=CE (MET) WARNING: (chiral) Have 1 chiral atoms that are inverted: WARNING: (chiral) A|186:CB(TPO) Weighted rms 0.0070 0.994 (temporary rms bond and angle for autobuster to pick up!) Initial Geometry Sanity Check Check for duplicate bonds: no duplicates found Check for duplicate or missing bond angles: all are OK Check for bond between an atom and itself not involving symmetry: all are OK There are not any bad contacts where Delta/sigma is greater than 6.5 Worst contact dist= 3.006 std= 3.840 sigma= 0.200 abs(Delta/sigma)= 4.169 ats A|198:CG (GLU) A|300:CG (PRO) It is likely that the geometry libraries, sequence info and links match the input molecule GEOMETRY CHECK OVERALL: PASS -type one : simply output final pdb file for compatibitilies with other options TLS information. Total number of groups: 0 Group Natoms FixRB FixTLS Group Tag Group Spec For final position, Geometry function summary term number weight rms GooF function fn/numb ================================================================================================ BOND bond lengths (angs) 4633 2.000 0.0070 0.348 1122.11 0.242 ANGL bond angles (degs) 6291 2.000 0.99 0.607 4637.98 0.737 TORS split-harmonic tors 1062 0.000 15.86 1.018 0.00 0.000 SINTOR sinusoidal tors 1062 2.000 15.86 1785.29 1.681 TRIG.onal planes (angs) 125 2.000 0.0027 0.137 4.72 0.038 PLAN general plane (angs) 649 5.000 0.0254 1.271 5241.36 8.076 BCORrelations (angs*2) 4633 20.000 6.814 1.157 124076.59 26.781 CONT (bad contacts) 0 5.000 0.00 IDEAL(ideal-dist contact) 5154 4.000 45579.44 CHIRAL (gelly semiharmon) 593 5.000 1948.42 SIM similarity restraint for NCS and/or TARGET 0.00 as none defined OCCSUM restraint on sum of occupanies 0.00 as none defined DISTAN utility restraints interatomic distance 0.00 as none defined UTILANGLE utility angle restraints 0.00 as none defined UTILTOR utility restraints on torsion angles 0.00 as none defined Peptide omega torsion angles 4.86 degs - monitor only WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: WARNING: 2 planes. Worst is 6.5 sigs 0.13 Angs A|176:C=A|176:CA=A|176:O=A|177:N=A|177:CA WARNING: 12 Bcorrel. Worst is 27.2 sigs 120.14 Angs**2 B|48:SD=CE (MET) WARNING: (chiral) Have 1 chiral atoms that are inverted: WARNING: (chiral) A|186:CB(TPO) Weighted rms 0.0070 0.994 (temporary rms bond and angle for autobuster to pick up!) s/r gelly normal terminationFinal Geometry Information (explanation)
2. Final results
Statistics and scale factors vs. cycle number (explanation) :
Average Figure of Merit (explanation) Structure Factor Amplitudes (explanation) # normal termination Program stopped.