Please reference use of the software as:
Version: 2.11.5 for linux64-ifort made on Nov 28 2012 at 00:53:37
Licenced to: Global Phasing Ltd (hypatia)
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. 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 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 = 0.15352E+02 B = -3.928 Setting starting scale K to value from Wilson scaling: 15.35164 Setting starting scale B to value from Wilson scaling: -3.92776Cycle 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 = 0.4787 Å2 to all atoms in fragment Added B = 0.4787 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 Nov 28 2012 00:52:24 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: -autoncs -screen \ 100 -screen_sigma \ 3.0 Setting up tnt routines including license check: TNT Stereochemistry Program Version: 5.23.5.0 Licence for Global Phasing Ltd (hypatia) 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 4710 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 10.57 Dictionary versions picked up from NOTE BUSTER_RESTRAINT_DICT cards as: ------ protgeo_eh99.dat (V1.8.2.3) 20120619 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 (V1.8.2.2) 20120418 COLLECTION OF NON-STANDARD AMINO ACIDS, MAINLY EH91 WITHOUT IDEAL DISTANCE INFO ------ nuclgeo.dat (V1.14.2.3) 20120611 ------ bcorrel.dat (V1.15) 20080423 ------ contact.dat (V1.20.2.3) 20121002 ------ idealdist_contact.dat (V1.7.2.4) 20121011 IDEAL-DISTANCE CONTACT TERM DATA AS USED IN PROLSQ. VALUES USED HERE ARE BASED ON THE REFMAC 5.5 IMPLEMENTATION. ------ restraints for A3P (ADENOSINE-3_-5_-DIPHOSPHATE) from cif dictionary A3P.grade_PDB_ligand.cif using refmacdict2tnt revision 1.23.2.11; generated by GRADE 1.2.0 from mol2 file /tmp/file0RSbRO.mol2 using mogul+qm ------ assume.dat (V1.10) 20110113 Have picked up spacegroup name for pdb output as 'P 21 21 2 ' Setting up Chain/Residue arrays Have command line specification -autoncs* Have found 1 NCS relations Pairwise matching residue number and type between chains: A B A . all B . Table key-- all : two chains have 100% match and same number of residues multi : ditto and they contribute to a multi chain ncs cluster ***% : two chains have >80% matching residue number/type - : chains appear to be unrelated chain A have identified ncs to 1 other chains. So will weight each autoncs by ( 2.000/#)= 2.0000 chain B have identified ncs to 1 other chains. So will weight each autoncs by ( 2.000/#)= 2.0000 For .Gelly cards produced see below - after pruning Setting up BUSTER_SET groups Have found 35 BUSTER_SET cards Now silently applying automatic/dictionary set definitions. For a verbose listing use '-verbose_set' flag. Applying user defined set definitions: =====NOTE BUSTER_SET ncsautoXcld = Water --> set 'ncsautoXcld' now has 0 atoms =====NOTE BUSTER_SET ncsautoABset = Chain_A \ ncsautoXcld --> set 'ncsautoABset' now has 2355 atoms Have defined 14 sets: set: 'All' has 4710 atoms in 572 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 4656 atoms in 570 residues - automatically defined set: 'Chain_A' has 2355 atoms in 286 residues - automatically defined set: 'Chain_B' has 2355 atoms in 286 residues - automatically defined set: 'Water' has 0 atoms in 0 residues - defined by dictionary file set: 'StdProtein' has 4656 atoms in 570 residues - defined by dictionary file set: 'Protein' has 4656 atoms in 570 residues - defined by dictionary file set: 'Back' has 2280 atoms in 570 residues - defined by dictionary file set: 'Side' has 2376 atoms in 542 residues - defined by dictionary file set: 'Other' has 54 atoms in 2 residues - defined by dictionary file set: 'ncsautoXcld' has 0 atoms in 0 residues - user specified set: 'ncsautoABset' has 2355 atoms in 286 residues - user specified No command line arguments '-occ_allhet' or '-occ_restyp' so will not setup automated occcupancy refinement Interpreting CONSTANT and FREE 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 = 4710 Before any COMBINE - Number of atoms with fixed BIJ = 4710 cf total number of atoms = 4710 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 WARNING ignoring pseudoCHIRAL centre A|293:CA(SER) A|293:N(SER) A|293:CB(SER) A|293:C(SER) WARNING .... as all three surrounding atoms are equivalent. WARNING ignoring pseudoCHIRAL centre B|293:CA(SER) B|293:N(SER) B|293:CB(SER) B|293:C(SER) WARNING .... as all three surrounding atoms are equivalent. NOTE BUSTER_CHIRAL_ANGLECUT card found - read value= -31.00 degs from it NOTE BUSTER_CHIRAL_SIGMA card found - read value= 1.70 degs from it 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 --- Have some similarity definitions Similarity restraints on RMSD use superposition routines from: Coutsias, E.A., Seok, C., Dill, K.A.(2004) "Using quaternions to calculate RMSD", J. Comput. Chem., 25:1849-1857 Have found 1 'NOTE BUSTER_SIM_DEFINE' cards Maximum number of chains involved in any SIM group (excluding the template)= 1 Interpreting card: NOTE BUSTER_SIM_DEFINE ncsautoAB ncsautoABset B Number of atoms in template set= 2355 Number of related chains (other than template) in SIM set= 1 List of chains to be restrained (excluding template)= B Pairwise RMSD, XYZ in Angstroms, for SIM group: ncsautoAB A B A ----- ----- B 0.645 ----- Overall RMSD,XYZ for the SIM group is 0.645 Angstroms Pairwise rms deviation of [individual B's minus their set/chain average] in Angs**2 A B Bavg A ----- ----- 37.89 B 8.08 ----- 43.97 Overall RMSD,B for the SIM group is 8.080 Angs**2 All the 2355 atoms in template are matched for each of the above fits transforms for each of the superpositions orthogonal matrix r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz (PDBSET syntax): TRANS_AB -0.999408 -0.034135 -0.004196 0.034183 -0.999346 -0.011774 -0.003792 -0.011911 0.999922 122.054 255.578 -34.861 reverse transforms TRANS_BA -0.999408 0.034183 -0.003792 -0.034135 -0.999346 -0.011911 -0.004196 -0.011774 0.999922 113.113 259.162 38.380 Setting up LSSR interatomic distance restraints Interpreting card: NOTE BUSTER_SIM_RESTRAIN_LSSR ncsautoAB 2.000 setting up interatomic distance pair restraints with: Dmin= 0.00 Dmax= 5.50 sigma= 0.20 Vmax= 10.00 weight= 2.00 number of distance pairs defined for this set is 30243 Have not supplied either '-sim_swap_equiv' or '-sim_swap_equiv_plus' argument so will not try swaping equivalent atoms to improve NCS and/or target agreement. NCS by LSSR outlier analysis -autoncs option automatic NCS prune routine -------- Residues pruned out by gradient condition: A|9 A|21 A|24 A|25 A|27 A|42 A|44 A|80 A|81 A|82 A|83 A|84 A|85 A|86 A|91 A|92 A|95 A|96 A|107 A|108 A|125 A|140 A|145 A|146 A|152 A|159 A|178 A|179 A|180 A|181 A|182 A|183 A|186 A|187 A|188 A|189 A|190 A|218 A|225 A|226 A|272 A|273 A|287 A|289 A|293 B|9 B|21 B|24 B|25 B|27 B|42 B|44 B|80 B|81 B|82 B|83 B|84 B|85 B|86 B|91 B|92 B|95 B|96 B|107 B|108 B|125 B|140 B|145 B|146 B|152 B|159 B|178 B|179 B|180 B|181 B|182 B|183 B|186 B|187 B|188 B|189 B|190 B|217 B|218 B|225 B|226 B|272 B|273 B|287 B|289 B|293 Residues pruned out by function/max condition: A|181! A|217 A|218! A|222 A|500 B|181! B|217! B|218! B|222 B|500 Total number of residues pruned out is 96 out of 572 participating Number of LSSR restraints pruned out is 9424 this is 31.2% of the total -autoncs .Gelly cards suitable for adaptation for manual definition/pruning (note auto pruning is done in a slightly different way so exact results may differ slightly) -autoncs option .Gelly cards also written to file auto_gelly_cards.txt NOTE BUSTER_SET ncsautoXcld = Water # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|9 A|21 A|24 A|25 A|27 A|42 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|44 A|80 A|81 A|82 A|83 A|84 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|85 A|86 A|91 A|92 A|95 A|96 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|107 A|108 A|125 A|140 A|145 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|146 A|152 A|159 A|178 A|179 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|180 A|181 A|182 A|183 A|186 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|187 A|188 A|189 A|190 A|217 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|218 A|222 A|225 A|226 A|272 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|273 A|287 A|289 A|293 A|500 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoABset = Chain_A \ ncsautoXcld # card added - produced by -autoncs NOTE BUSTER_SIM_DEFINE ncsautoAB ncsautoABset B # card added - produced by -autoncs NOTE BUSTER_SIM_RESTRAIN_LSSR ncsautoAB 2.000 # card added - produced by -autoncs LSSR function contribution before pruning 52637.9 after pruning 5705.0 Graph of which residues pruned from LSSR: ncs_pruned.mtv Graph of LSSR function outliers ncs_function_outliers.mtv Graph of LSSR gradient outliers ncs_gradient_outliers.mtv LSSR - analysis of distance difference distribution for NCS DeltaD less than 0.5 Angs: proportion of population= 98.98% average DeltaD of subset 0.010 Angs Histogram of LSSR deltaD distribution ncs_histogram.mtv No 'NOTE BUSTER_TLS_SET' cards found - so no TLS constraints will be used Number of parameters to describe molecular conformation = 18840 Number of free parameters to be adjusted in refinement = 18840 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 0.100 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 All atoms matched for ccp4 atom type. Number of ccp4 atom types used is 25 (H-bound and not H-bound counted separately) Setting up short/ideal-distance contacts Using gelly special position handling. (For TNT instead rerun with argument '-special_tnt') TERM weight number TNT_fn Gelly_fn diff BOND 2.000 4856 2461.449 2461.449 0.000 ANGL 2.000 6604 5964.000 5964.000 0.000 IMPR 0.000 0 0.000 0.000 0.000 TORS 2.000 1664 3975.424 3975.424 0.000 TRIG 2.000 114 20.156 20.156 0.000 PLAN 5.000 708 1828.754 1828.754 0.000 CONT 5.000 0 222.923 0.000 222.923 BCOR 20.000 4798 6416.489 6416.489 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 add a default BCOR for bond A|500:P1(A3P) A|500:O1P(A3P) add a default BCOR for bond A|500:P1(A3P) A|500:O2P(A3P) add a default BCOR for bond A|500:P1(A3P) A|500:O3'(A3P) add a default BCOR for bond A|500:P1(A3P) A|500:O3P(A3P) add a default BCOR for bond A|500:P2(A3P) A|500:O4P(A3P) add a default BCOR for bond A|500:P2(A3P) A|500:O5'(A3P) add a default BCOR for bond A|500:P2(A3P) A|500:O5P(A3P) add a default BCOR for bond A|500:P2(A3P) A|500:O6P(A3P) add a default BCOR for bond A|500:O5'(A3P) A|500:C5'(A3P) add a default BCOR for bond A|500:C5'(A3P) A|500:C4'(A3P) add a default BCOR for bond A|500:C4'(A3P) A|500:C3'(A3P) add a default BCOR for bond A|500:C4'(A3P) A|500:O4'(A3P) add a default BCOR for bond A|500:O4'(A3P) A|500:C1'(A3P) add a default BCOR for bond A|500:C3'(A3P) A|500:C2'(A3P) add a default BCOR for bond A|500:C3'(A3P) A|500:O3'(A3P) add a default BCOR for bond A|500:C2'(A3P) A|500:C1'(A3P) add a default BCOR for bond A|500:C2'(A3P) A|500:O2'(A3P) add a default BCOR for bond A|500:C1'(A3P) A|500:N9(A3P) add a default BCOR for bond A|500:N9(A3P) A|500:C4(A3P) add a default BCOR for bond A|500:N9(A3P) A|500:C8(A3P) add a default BCOR for bond A|500:C8(A3P) A|500:N7(A3P) add a default BCOR for bond A|500:N7(A3P) A|500:C5(A3P) add a default BCOR for bond A|500:C5(A3P) A|500:C4(A3P) add a default BCOR for bond A|500:C5(A3P) A|500:C6(A3P) add a default BCOR for bond A|500:C6(A3P) A|500:N1(A3P) add a default BCOR for bond A|500:C6(A3P) A|500:N6(A3P) add a default BCOR for bond A|500:N1(A3P) A|500:C2(A3P) add a default BCOR for bond A|500:C2(A3P) A|500:N3(A3P) add a default BCOR for bond A|500:N3(A3P) A|500:C4(A3P) add a default BCOR for bond B|500:P1(A3P) B|500:O1P(A3P) add a default BCOR for bond B|500:P1(A3P) B|500:O2P(A3P) add a default BCOR for bond B|500:P1(A3P) B|500:O3'(A3P) add a default BCOR for bond B|500:P1(A3P) B|500:O3P(A3P) add a default BCOR for bond B|500:P2(A3P) B|500:O4P(A3P) add a default BCOR for bond B|500:P2(A3P) B|500:O5'(A3P) add a default BCOR for bond B|500:P2(A3P) B|500:O5P(A3P) add a default BCOR for bond B|500:P2(A3P) B|500:O6P(A3P) add a default BCOR for bond B|500:O5'(A3P) B|500:C5'(A3P) add a default BCOR for bond B|500:C5'(A3P) B|500:C4'(A3P) add a default BCOR for bond B|500:C4'(A3P) B|500:C3'(A3P) only first 40 added listed here Have added a total of 58 bcorrels for bonds which do not already have a bcorrel 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 568 Number of other torsion is 1096 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 -4.22 degrees Fix up bond A|102:CA=CB (PRO) ideal from 1.531 to 1.533 actual= 1.534, sigma from 0.020 to 0.018 Angs Fix up bond A|102:CB=CG (PRO) ideal from 1.495 to 1.506 actual= 1.503, sigma from 0.050 to 0.039 Angs Fix up bond A|102:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.518, 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= 127.7, 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= 120.5, 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= 103.0, 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= 114.6, 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= 105.1, 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= 106.2, 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= 104.7, 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= 111.7, 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 -2.82 degrees Fix up bond B|102:CA=CB (PRO) ideal from 1.531 to 1.533 actual= 1.531, sigma from 0.020 to 0.018 Angs Fix up bond B|102:CB=CG (PRO) ideal from 1.495 to 1.506 actual= 1.517, sigma from 0.050 to 0.039 Angs Fix up bond B|102:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.515, sigma from 0.033 to 0.027 Angs Fix up bond B|102:CD=N (PRO) ideal from 1.474 to 1.474 actual= 1.479, 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= 127.4, 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= 120.4, 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= 103.2, 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= 114.8, 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= 105.1, 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= 106.8, 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= 104.5, 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= 112.1, 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 = 6.539138E+05 rms gradient= 72.9300 X-ray contribution to function value = 5.973778E+05 Geometry contribution (inc ncs) = 56535.9 Geometry function summary term number weight rms GooF function fn/numb ================================================================================================ BOND bond lengths (angs) 4856 2.000 0.0098 0.503 2460.53 0.507 ANGL bond angles (degs) 6604 2.000 1.05 0.662 5783.28 0.876 TORS split-harmonic tors 1096 0.000 21.28 1.347 0.00 0.000 SINTOR sinusoidal tors 1096 2.000 21.28 2794.54 2.550 TRIG.onal planes (angs) 114 2.000 0.0059 0.297 20.16 0.177 PLAN general plane (angs) 708 5.000 0.0144 0.719 1828.75 2.583 BCORrelations (angs*2) 4856 20.000 1.512 0.257 6416.49 1.321 CONT (bad contacts) 0 5.000 0.00 IDEAL(ideal-dist contact) 5206 4.000 31460.16 CHIRAL (gelly semiharmon) 598 5.000 67.00 SIM similarity restraint for NCS and/or TARGET 5705.01 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 2.73 degs - monitor only Weighted rms 0.0098 1.051 (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= 2.174 std= 3.340 sigma= 0.200 abs(Delta/sigma)= 5.829 ats B|193:OH (TYR) B|500:C2 (A3P) It is likely that the geometry libraries, sequence info and links match the input molecule GEOMETRY CHECK OVERALL: PASS TAO: Toolkit for Advanced Optimization. Reference: Benson, S.J., McInnes, L.C., More, J., Sarich, J. (2005) "TAO User Manual (Revision 1.8)", Mathematics and Computer Science Division, Argonne National Laboratory ANL/MCS-TM-242, http://www.mcs.anl.gov/tao Will write writing pdb file every 10 its during opt (overide by -keeppdb value) Will apply TAO optimization Maximum number of iterations 20 Convergence test on Grms 4.0000 (-glim) Limit on rms displacement to original position (rmsD2init): NONE test inactive (-dlim) MaxLik Scaling Cycle 0003 (explanation) Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init Opttag_H 0 6.539138E+05 5.973778E+05 56535.9 72.9300 0.000000E+00 0.000000E+00 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0004 (explanation) MaxLik Scaling Cycle 0005 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 001 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
1 6.518705E+05 5.942593E+05 57611.3 116.481 0.00432493 0.100259 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0006 (explanation)
MaxLik Scaling Cycle 0007 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 002 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
2 6.512372E+05 5.939531E+05 57284.1 91.9071 0.00483410 0.113846 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0008 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 003 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
3 6.507901E+05 5.939712E+05 56818.9 64.3780 0.00460796 0.107317 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0009 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 004 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
4 6.502136E+05 5.937410E+05 56472.6 50.4295 0.00496604 0.109138 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0010 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 005 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
5 6.493758E+05 5.927881E+05 56587.7 94.2745 0.00726937 0.140242 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0011 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 006 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
6 6.485916E+05 5.919325E+05 56659.1 65.1387 0.0100062 0.177506 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0012 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 007 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
7 6.482014E+05 5.913016E+05 56899.8 79.4105 0.0128549 0.213321 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0013 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 008 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
8 6.479390E+05 5.911775E+05 56761.5 41.0313 0.0135692 0.219535 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0014 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 009 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
9 6.477681E+05 5.911209E+05 56647.1 38.7498 0.0138313 0.214906 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0015 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 010 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
10 6.473930E+05 5.909218E+05 56471.1 57.7063 0.0148963 0.234289 Opttag_D
Writing pdb file to gelly_output_iter000010.pdb
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0016 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 011 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
11 6.470842E+05 5.906150E+05 56469.2 84.8757 0.0170457 0.275353 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0017 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 012 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
12 6.467893E+05 5.904757E+05 56313.7 44.8222 0.0181471 0.295335 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0018 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 013 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
13 6.465480E+05 5.902995E+05 56248.6 28.0797 0.0195925 0.320440 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0019 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 014 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
14 6.464370E+05 5.902077E+05 56229.3 27.9731 0.0203902 0.334297 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0020 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 015 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
15 6.462500E+05 5.900019E+05 56248.1 47.5241 0.0221745 0.367556 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0021 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 016 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
16 6.461480E+05 5.898117E+05 56336.3 43.2545 0.0240511 0.401299 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0022 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 017 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
17 6.460492E+05 5.898299E+05 56219.2 21.0772 0.0236755 0.394766 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0023 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 018 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
18 6.459631E+05 5.897990E+05 56164.1 22.1101 0.0237163 0.395581 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0024 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 019 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
19 6.458517E+05 5.896932E+05 56158.5 25.8950 0.0245621 0.410000 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0025 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 020 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
20 6.456717E+05 5.894757E+05 56196.0 26.9351 0.0268181 0.446774 Opttag_D
Geometry Restraint Deviations SCREEN Information
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) 4856 2.000 0.0101 0.518 2606.20 0.537
ANGL bond angles (degs) 6604 2.000 1.06 0.664 5830.19 0.883
TORS split-harmonic tors 1096 0.000 21.25 1.344 0.00 0.000
SINTOR sinusoidal tors 1096 2.000 21.25 2786.62 2.543
TRIG.onal planes (angs) 114 2.000 0.0060 0.299 20.38 0.179
PLAN general plane (angs) 708 5.000 0.0145 0.727 1870.38 2.642
BCORrelations (angs*2) 4856 20.000 1.558 0.265 6812.31 1.403
CONT (bad contacts) 0 5.000 0.00
IDEAL(ideal-dist contact) 5185 4.000 30847.34
CHIRAL (gelly semiharmon) 598 5.000 66.09
SIM similarity restraint for NCS and/or TARGET 5356.52
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 2.75 degs - monitor only
Weighted rms 0.0101 1.055 (temporary rms bond and angle for autobuster to pick up!)
Outputing geometry progress graph in plotmtv format to file:Geom_Res.mtv
s/r gelly normal termination
Statistics and scale factors vs. cycle number (explanation) :
Final 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.