Please reference use of the software as:
Version: 2.8.0 for linux-ifort made on Jul 22 2009 at 02:57:53
Licenced to: Global Phasing Ltd (newton-old)
Parsing of the BUSTER cardfile
TITLE : autoBUSTER refinement Cell information (explanation) 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: 21874 Number of accepted reflexions: 21019 Number of rejected reflexions: 855 Reflexions in test set: 1669 (explanation) Reflexions in working set: 19350 (explanation)
1. Generating initial model
2.10 * Shannon sampling rate. NX NY NZ: 128 240 120 Effective Shannon rates are: 2.13 2.55 2.22 Allocated BUFFER of size: 14.282 Mb. Allocated BUFAUX of size: 14.282 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 1.23848) ... 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 = 0.15259E+02 B = -5.397Cycle 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 = 0.1524 Å2 to all atoms in fragment Added B = 0.1524 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 Jul 22 2009 02:55:39 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 Control flags set to: -type one \ -screen 100 \ -screen_sigma 3.0 Setting up tnt routines including license check: TNT Stereochemistry Program Version: 5.20.0.0 Licence for Global Phasing Ltd (newton-old) is valid 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 4217 atoms from TNT to gelly's store 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 (V1.6) 20090612 STANDARD AMINO ACID DICTIONARY. BONDS AND ANGLES FROM ENGH AND HUBER EH99. OTHER VALUES BASED ON PREVIOUS TNT OR TAKEN FROM CCP4. ------ exoticaa.dat (V1.3.2.1) 20090706 COLLECTION OF NON-STANDARD AMINO ACIDS, MAINLY EH91 WITHOUT IDEAL DISTANCE INFO ------ nuclgeo.dat (V1.13) 20090617 ------ bcorrel.dat (V1.15) 20080423 ------ contact.dat (V1.15) 20070207 ------ idealdist_contact.dat (V1.3.2.1) 20090706 IDEAL-DISTANCE CONTACT TERM DATA AS USED IN PROLSQ. VALUES USED HERE ARE BASED ON THE REFMAC 5.5 IMPLEMENTATION. ------ assume.dat (V1.9) 20090602 Have picked up spacegroup name for pdb output as 'P 21 21 2 ' 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 4217 atoms in 562 residues - automatically defined set: 'Empty' has 0 atoms in 0 residues - automatically defined set: 'ExoticAA' has 0 atoms in 0 residues - defined by dictionary file set: 'NotHET' has 4215 atoms in 560 residues - automatically defined set: 'Chain_A' has 2109 atoms in 281 residues - automatically defined set: 'Chain_B' has 2108 atoms in 281 residues - automatically defined set: 'Water' has 0 atoms in 0 residues - defined by dictionary file set: 'StdProtein' has 4217 atoms in 562 residues - defined by dictionary file set: 'Protein' has 4217 atoms in 562 residues - defined by dictionary file set: 'Back' has 2241 atoms in 562 residues - defined by dictionary file set: 'Side' has 1976 atoms in 532 residues - defined by dictionary file set: 'Other' has 0 atoms in 0 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 = 4217 Before any COMBINE - Number of atoms with fixed BIJ = 4217 cf total number of atoms = 4217 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 = 16868 Number of free parameters to be adjusted in refinement = 16868 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 -X,-Y,Z 3555 1/2-X,1/2+Y,-Z 4555 1/2+X,1/2-Y,-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 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 matched 21 residue-type records and will use 20 ccp4 energy atomtypes All atoms matched for ccp4 atom type - so ideal contact will be used for all contacts (rather than TNT short). Using gelly special position handling. (For TNT instead rerun with argument '-special_tnt') TERM weight number TNT_fn Gelly_fn diff BOND 2.000 4311 18941.486 18941.486 0.000 ANGL 2.000 5778 18922.969 18922.969 0.000 IMPR 0.000 0 0.000 0.000 0.000 TORS 2.000 1400 3054.121 3054.121 0.000 TRIG 2.000 64 0.283 0.283 0.000 PLAN 5.000 610 629.638 629.638 0.000 CONT 5.000 0 27400.283 0.000 27400.283 BCOR 20.000 4311 16444.050 16444.050 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 Torsion angles split into peptide omega and other Number of peptide omega angles is 556 Number of other torsion is 844 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|102 because omega torsion A|101:CA(PRO)=A|101:C(PRO)=A|102:N(PRO)=A|102:CA(PRO) is 0.08 degrees Fix up bond A|102:CA=CB (PRO) ideal from 1.531 to 1.533 actual= 1.524, sigma from 0.020 to 0.018 Angs Fix up bond A|102:CB=CG (PRO) ideal from 1.495 to 1.506 actual= 1.495, sigma from 0.050 to 0.039 Angs Fix up bond A|102:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.514, sigma from 0.033 to 0.027 Angs Fix up bond A|102:CD=N (PRO) ideal from 1.474 to 1.474 actual= 1.479, sigma from 0.014 to 0.014 Angs Fix up angle A|101:C(PRO)=A|102:N(PRO)=A|102:CA(PRO) ideal from 119.3 to 127.0 actual= 128.8, sigma from 1.5 to 2.4 Degs Fix up angle A|101:C(PRO)=A|102:N(PRO)=A|102:CD(PRO) ideal from 128.4 to 120.6 actual= 119.6, sigma from 2.1 to 2.2 Degs Fix up angle A|102:N=CA=CB (PRO) ideal from 103.3 to 102.6 actual= 103.6, sigma from 1.2 to 1.1 Degs Fix up angle A|102:CB=CA=C (PRO) ideal from 111.7 to 112.0 actual= 111.3, sigma from 2.1 to 2.5 Degs Fix up angle A|102:CA=CB=CG (PRO) ideal from 104.8 to 104.0 actual= 104.4, sigma from 1.9 to 1.9 Degs Fix up angle A|102:CB=CG=CD (PRO) ideal from 106.5 to 105.4 actual= 107.1, sigma from 3.9 to 2.3 Degs Fix up angle A|102:CG=CD=N (PRO) ideal from 103.2 to 103.8 actual= 103.9, sigma from 1.5 to 1.2 Degs Fix up angle A|102:CA=N=CD (PRO) ideal from 111.7 to 111.5 actual= 111.6, sigma from 1.4 to 1.4 Degs Apply the fix to cis PRO residue B|102 because omega torsion B|101:CA(PRO)=B|101:C(PRO)=B|102:N(PRO)=B|102:CA(PRO) is -0.02 degrees Fix up bond B|102:CA=CB (PRO) ideal from 1.531 to 1.533 actual= 1.525, sigma from 0.020 to 0.018 Angs Fix up bond B|102:CB=CG (PRO) ideal from 1.495 to 1.506 actual= 1.495, sigma from 0.050 to 0.039 Angs Fix up bond B|102:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.514, sigma from 0.033 to 0.027 Angs Fix up bond B|102:CD=N (PRO) ideal from 1.474 to 1.474 actual= 1.478, sigma from 0.014 to 0.014 Angs Fix up angle B|101:C(PRO)=B|102:N(PRO)=B|102:CA(PRO) ideal from 119.3 to 127.0 actual= 128.7, sigma from 1.5 to 2.4 Degs Fix up angle B|101:C(PRO)=B|102:N(PRO)=B|102:CD(PRO) ideal from 128.4 to 120.6 actual= 119.7, sigma from 2.1 to 2.2 Degs Fix up angle B|102:N=CA=CB (PRO) ideal from 103.3 to 102.6 actual= 103.6, sigma from 1.2 to 1.1 Degs Fix up angle B|102:CB=CA=C (PRO) ideal from 111.7 to 112.0 actual= 111.2, sigma from 2.1 to 2.5 Degs Fix up angle B|102:CA=CB=CG (PRO) ideal from 104.8 to 104.0 actual= 104.4, sigma from 1.9 to 1.9 Degs Fix up angle B|102:CB=CG=CD (PRO) ideal from 106.5 to 105.4 actual= 107.1, sigma from 3.9 to 2.3 Degs Fix up angle B|102:CG=CD=N (PRO) ideal from 103.2 to 103.8 actual= 103.9, sigma from 1.5 to 1.2 Degs Fix up angle B|102:CA=N=CD (PRO) ideal from 111.7 to 111.5 actual= 111.6, sigma from 1.4 to 1.4 Degs Weight for ideal-distance contact term= 4.000 MaxLik Scaling Cycle 0002 (explanation) Initial functional value = 4.029679E+05 rms gradient= 429.718 X-ray contribution to function value = 2.740110E+05 Geometry contribution (inc ncs) = 1.289569E+05 Geometry function summary term number weight rms GooF function fn/numb ================================================================================================ BOND bond lengths (angs) 4311 2.000 0.0293 1.482 18941.80 4.394 ANGL bond angles (degs) 5778 2.000 2.07 1.272 18701.48 3.237 TORS split-harmonic tors 844 0.000 20.93 1.345 0.00 0.000 SINTOR sinusoidal tors 844 2.000 20.93 2111.76 2.502 TRIG.onal planes (angs) 64 2.000 0.0009 0.047 0.28 0.004 PLAN general plane (angs) 610 5.000 0.0091 0.454 629.64 1.032 BCORrelations (angs*2) 4311 20.000 2.536 0.437 16444.05 3.814 CONT (bad contacts) 0 5.000 0.00 IDEAL(ideal-dist contact) 4589 4.000 56851.58 CHIRAL (gelly semiharmon) 557 5.000 15276.32 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 1.45 degs - monitor only WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: WARNING: 80 bond lengths. Worst is 19.0 sigs 1.23 Angs A|151:CG=CD (GLU) WARNING: 90 bond angles. Worst is 16.1 sigs 111.35 degs B|23:CB=CG=CD1 (TYR) WARNING: 67 idealD contacts. Worst 16.3 sigs 0.29 Angs A|89:CA(GLU)=A|90:N(PRO) symm: 1555=2675 WARNING: (chiral) Have 8 chiral atoms that are inverted: WARNING: (chiral) A|57:CB(ILE) A|105:CB(ILE) A|204:CB(ILE) A|252:CB(ILE) B|57:CB(ILE) B|105:CB(ILE) B|204:CB(ILE) B|252:CB(ILE) Weighted rms 0.0293 2.072 (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 There are at least 20 bad contacts where Delta/sigma is greater than 6.5 Looking at each one of the first 20 in turn to see whether it is likely to indicate a setup problem with geometry restraints. 1 dist= 0.29 idealD= 3.55 sigma= 0.20 abs(Delta/sigma)= 16.30 Between atoms A|89:CA (GLU) A|90:N (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 2 dist= 0.94 idealD= 3.50 sigma= 0.20 abs(Delta/sigma)= 12.78 Between atoms A|89:C (GLU) A|89:C (GLU) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 3 dist= 1.20 idealD= 3.70 sigma= 0.20 abs(Delta/sigma)= 12.49 Between atoms A|89:CA (GLU) A|89:C (GLU) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 4 dist= 1.50 idealD= 3.90 sigma= 0.20 abs(Delta/sigma)= 11.99 Between atoms A|89:CA (GLU) A|90:CA (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 5 dist= 1.11 idealD= 3.44 sigma= 0.20 abs(Delta/sigma)= 11.65 Between atoms A|86:OD2 (ASP) A|87:CG (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 6 dist= 1.55 idealD= 3.84 sigma= 0.20 abs(Delta/sigma)= 11.45 Between atoms A|88:CA (GLY) A|90:CG (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 7 dist= 1.50 idealD= 3.67 sigma= 0.20 abs(Delta/sigma)= 10.85 Between atoms A|88:C (GLY) A|90:CG (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 8 dist= 1.44 idealD= 3.52 sigma= 0.20 abs(Delta/sigma)= 10.38 Between atoms A|89:CB (GLU) A|90:N (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 9 dist= 1.48 idealD= 3.54 sigma= 0.20 abs(Delta/sigma)= 10.32 Between atoms B|111:N (LEU) B|111:CD1 (LEU) is a contact within a residue - so probably just a distorted residue? 10 dist= 1.48 idealD= 3.54 sigma= 0.20 abs(Delta/sigma)= 10.32 Between atoms A|111:N (LEU) A|111:CD1 (LEU) is a contact within a residue - so probably just a distorted residue? 11 dist= 1.48 idealD= 3.54 sigma= 0.20 abs(Delta/sigma)= 10.32 Between atoms A|215:N (LEU) A|215:CD1 (LEU) is a contact within a residue - so probably just a distorted residue? 12 dist= 1.48 idealD= 3.54 sigma= 0.20 abs(Delta/sigma)= 10.32 Between atoms B|215:N (LEU) B|215:CD1 (LEU) is a contact within a residue - so probably just a distorted residue? 13 dist= 1.57 idealD= 3.57 sigma= 0.20 abs(Delta/sigma)= 10.02 Between atoms A|180:CZ2 (TRP) A|184:CZ (ARG) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 14 dist= 1.45 idealD= 3.44 sigma= 0.20 abs(Delta/sigma)= 9.97 Between atoms A|86:OD2 (ASP) A|87:CB (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 15 dist= 1.26 idealD= 3.20 sigma= 0.20 abs(Delta/sigma)= 9.71 Between atoms A|89:N (GLU) A|90:N (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 16 dist= 2.07 idealD= 3.87 sigma= 0.20 abs(Delta/sigma)= 9.01 Between atoms A|89:CB (GLU) A|90:CA (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 17 dist= 1.85 idealD= 3.55 sigma= 0.20 abs(Delta/sigma)= 8.52 Between atoms A|89:N (GLU) A|90:CA (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 18 dist= 2.01 idealD= 3.67 sigma= 0.20 abs(Delta/sigma)= 8.32 Between atoms A|89:CD (GLU) A|91:CB (SER) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 19 dist= 1.80 idealD= 3.44 sigma= 0.20 abs(Delta/sigma)= 8.20 Between atoms A|89:CB (GLU) A|90:O (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. 20 dist= 1.72 idealD= 3.35 sigma= 0.20 abs(Delta/sigma)= 8.17 Between atoms A|89:C (GLU) A|90:N (PRO) The contact is between two atoms via a symmetry operator, hopefully refinement will fix this. GEOMETRY CHECK OVERALL: WARN Have -type card that specifies calculation type 'one' 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.