Please reference use of the software as:
Version: 2.11.0 for linux64-ifort made on Jul 21 2010 at 00:59:16
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. 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 = 0.14732E+02 B = -4.574 Setting starting scale K to value from Wilson scaling: 14.73176 Setting starting scale B to value from Wilson scaling: -4.57356Cycle 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 = 0.4089 Å2 to all atoms in fragment Added B = 0.4089 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 21 2010 00:57:02 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: 5.23.0.0 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 4572 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 11.25 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 (V1.8) 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 (V1.16) 20100211 ------ idealdist_contact.dat (V1.6) 20100218 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 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 34 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 2290 atoms Have defined 14 sets: set: 'All' has 4572 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 4570 atoms in 560 residues - automatically defined set: 'Chain_A' has 2290 atoms in 281 residues - automatically defined set: 'Chain_B' has 2282 atoms in 281 residues - automatically defined set: 'Water' has 0 atoms in 0 residues - defined by dictionary file set: 'StdProtein' has 4572 atoms in 562 residues - defined by dictionary file set: 'Protein' has 4572 atoms in 562 residues - defined by dictionary file set: 'Back' has 2241 atoms in 562 residues - defined by dictionary file set: 'Side' has 2331 atoms in 534 residues - defined by dictionary file set: 'Other' has 0 atoms in 0 residues - defined by dictionary file set: 'ncsautoXcld' has 0 atoms in 0 residues - user specified set: 'ncsautoABset' has 2290 atoms in 281 residues - user specified 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 = 4572 Before any COMBINE - Number of atoms with fixed BIJ = 4572 cf total number of atoms = 4572 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 --- 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= 2290 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 0.751 ----- Overall RMSD,XYZ for the SIM group is 0.751 Angstroms Pairwise rms deviation of [individual B's minus their set/chain average] in Angs**2 A B Bavg A ----- ----- 38.87 B 7.67 ----- 45.08 Overall RMSD,B for the SIM group is 7.672 Angs**2 The number of common atoms for the above fits: A B A ----- ----- B 2282 ----- (compared to the template set that has 2290 atoms in it) List of atoms that are absent in one or more chains for this group: A B N 7 + - CG2 7 + - CG 184 + - CD 184 + - NE 184 + - CZ 184 + - NH1 184 + - NH2 184 + - (key + atom present for this chain - atom absent for this chain) transforms for each of the superpositions orthogonal matrix r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz (PDBSET syntax): TRANS_AB -0.999537 -0.030145 -0.004144 0.030189 -0.999485 -0.010886 -0.003813 -0.011006 0.999932 121.599 255.867 -34.959 reverse transforms TRANS_BA -0.999537 0.030189 -0.003813 -0.030145 -0.999485 -0.011006 -0.004144 -0.010886 0.999932 113.685 259.017 38.246 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 29011 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|11 A|12 A|13 A|19 A|20 A|21 A|30 A|57 A|58 A|81 A|82 A|83 A|84 A|85 A|92 A|93 A|94 A|96 A|105 A|106 A|107 A|108 A|117 A|121 A|123 A|132 A|141 A|144 A|145 A|146 A|149 A|155 A|159 A|178 A|183 A|186 A|188 A|200 A|207 A|208 A|223 A|242 A|269 A|273 B|7 B|11 B|12 B|13 B|19 B|20 B|21 B|30 B|57 B|58 B|81 B|82 B|83 B|84 B|85 B|92 B|93 B|94 B|96 B|105 B|106 B|107 B|108 B|117 B|121 B|123 B|132 B|141 B|144 B|145 B|146 B|149 B|155 B|159 B|178 B|183 B|184 B|186 B|188 B|200 B|207 B|208 B|223 B|269 B|273 Residues pruned out by function/max condition: A|12! A|72 A|85! A|86 A|87 A|88 A|89 A|90 A|91 A|94! A|122 A|123! A|215 A|216 A|217 A|218 A|219 A|220 A|222 B|12! B|72 B|85! B|86 B|87 B|88 B|89 B|90 B|91 B|94! B|122 B|123! B|215 B|216 B|217 B|218 B|219 B|220 B|222 Total number of residues pruned out is 119 out of 561 participating Number of LSSR restraints pruned out is 10319 this is 35.6% 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|11 A|12 A|13 A|19 A|20 A|21 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|30 A|57 A|58 A|72 A|81 A|82 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|83 A|84 A|85 A|86 A|87 A|88 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|89 A|90 A|91 A|92 A|93 A|94 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|96 A|105 A|106 A|107 A|108 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|117 A|121 A|122 A|123 A|132 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|141 A|144 A|145 A|146 A|149 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|155 A|159 A|178 A|183 A|186 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|188 A|200 A|207 A|208 A|215 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|216 A|217 A|218 A|219 A|220 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { A|222 A|223 A|242 A|269 A|273 } # 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 78405.7 after pruning 11039.9 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= 97.73% average DeltaD of subset 0.013 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 = 18288 Number of free parameters to be adjusted in refinement = 18288 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 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 - so ideal contact will be used for all contacts (rather than TNT short). Number of ccp4 atom types used is 20 (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 4712 2635.658 2635.658 0.000 ANGL 2.000 6399 8323.901 8323.901 0.000 IMPR 0.000 0 0.000 0.000 0.000 TORS 2.000 1600 4320.591 4320.591 0.000 TRIG 2.000 110 30.405 30.405 0.000 PLAN 5.000 665 2001.403 2001.403 0.000 CONT 5.000 0 52.777 0.000 52.777 BCOR 20.000 4712 6782.714 6782.714 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 556 Number of other torsion is 1044 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|90 because omega torsion A|89:CA(GLU)=A|89:C(GLU)=A|90:N(PRO)=A|90:CA(PRO) is -5.98 degrees Fix up bond A|90:CA=CB (PRO) ideal from 1.531 to 1.533 actual= 1.543, sigma from 0.020 to 0.018 Angs Fix up bond A|90:CB=CG (PRO) ideal from 1.495 to 1.506 actual= 1.536, sigma from 0.050 to 0.039 Angs Fix up bond A|90:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.523, sigma from 0.033 to 0.027 Angs Fix up bond A|90:CD=N (PRO) ideal from 1.474 to 1.474 actual= 1.480, sigma from 0.014 to 0.014 Angs Fix up angle A|89:C(GLU)=A|90:N(PRO)=A|90:CA(PRO) ideal from 119.3 to 127.0 actual= 129.0, sigma from 1.5 to 2.4 Degs Fix up angle A|89:C(GLU)=A|90:N(PRO)=A|90:CD(PRO) ideal from 128.4 to 120.6 actual= 121.6, sigma from 2.1 to 2.2 Degs Fix up angle A|90:N=CA=CB (PRO) ideal from 103.3 to 102.6 actual= 102.9, sigma from 1.2 to 1.1 Degs Fix up angle A|90:CB=CA=C (PRO) ideal from 111.7 to 112.0 actual= 115.0, sigma from 2.1 to 2.5 Degs Fix up angle A|90:CA=CB=CG (PRO) ideal from 104.8 to 104.0 actual= 104.5, sigma from 1.9 to 1.9 Degs Fix up angle A|90:CB=CG=CD (PRO) ideal from 106.5 to 105.4 actual= 108.0, sigma from 3.9 to 2.3 Degs Fix up angle A|90:CG=CD=N (PRO) ideal from 103.2 to 103.8 actual= 103.7, sigma from 1.5 to 1.2 Degs Fix up angle A|90:CA=N=CD (PRO) ideal from 111.7 to 111.5 actual= 109.1, sigma from 1.4 to 1.4 Degs 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 -4.85 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= 1.499, sigma from 0.050 to 0.039 Angs Fix up bond A|102:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.517, 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= 127.6, 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= 120.6, 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= 103.2, 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= 114.9, 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= 106.4, 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= 104.6, 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|87 because omega torsion B|86:CA(ASP)=B|86:C(ASP)=B|87:N(PRO)=B|87:CA(PRO) is -0.41 degrees Fix up bond B|87:CA=CB (PRO) ideal from 1.531 to 1.533 actual= 1.543, sigma from 0.020 to 0.018 Angs Fix up bond B|87:CB=CG (PRO) ideal from 1.495 to 1.506 actual= 1.540, sigma from 0.050 to 0.039 Angs Fix up bond B|87:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.528, sigma from 0.033 to 0.027 Angs Fix up bond B|87:CD=N (PRO) ideal from 1.474 to 1.474 actual= 1.475, sigma from 0.014 to 0.014 Angs Fix up angle B|86:C(ASP)=B|87:N(PRO)=B|87:CA(PRO) ideal from 119.3 to 127.0 actual= 130.4, sigma from 1.5 to 2.4 Degs Fix up angle B|86:C(ASP)=B|87:N(PRO)=B|87:CD(PRO) ideal from 128.4 to 120.6 actual= 120.0, sigma from 2.1 to 2.2 Degs Fix up angle B|87: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 B|87:CB=CA=C (PRO) ideal from 111.7 to 112.0 actual= 115.2, sigma from 2.1 to 2.5 Degs Fix up angle B|87:CA=CB=CG (PRO) ideal from 104.8 to 104.0 actual= 105.7, sigma from 1.9 to 1.9 Degs Fix up angle B|87:CB=CG=CD (PRO) ideal from 106.5 to 105.4 actual= 107.2, sigma from 3.9 to 2.3 Degs Fix up angle B|87:CG=CD=N (PRO) ideal from 103.2 to 103.8 actual= 103.3, sigma from 1.5 to 1.2 Degs Fix up angle B|87:CA=N=CD (PRO) ideal from 111.7 to 111.5 actual= 109.6, 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 -3.56 degrees Fix up bond B|102:CA=CB (PRO) ideal from 1.531 to 1.533 actual= 1.530, sigma from 0.020 to 0.018 Angs Fix up bond B|102:CB=CG (PRO) ideal from 1.495 to 1.506 actual= 1.510, sigma from 0.050 to 0.039 Angs Fix up bond B|102:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.513, sigma from 0.033 to 0.027 Angs Fix up bond B|102:CD=N (PRO) ideal from 1.474 to 1.474 actual= 1.477, 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= 120.5, 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= 103.3, 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= 115.2, 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= 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 Apply the fix to cis PRO residue B|216 because omega torsion B|215:CA(LEU)=B|215:C(LEU)=B|216:N(PRO)=B|216:CA(PRO) is -2.31 degrees Fix up bond B|216:CA=CB (PRO) ideal from 1.531 to 1.533 actual= 1.537, sigma from 0.020 to 0.018 Angs Fix up bond B|216:CB=CG (PRO) ideal from 1.495 to 1.506 actual= 1.540, sigma from 0.050 to 0.039 Angs Fix up bond B|216:CG=CD (PRO) ideal from 1.502 to 1.512 actual= 1.511, sigma from 0.033 to 0.027 Angs Fix up bond B|216:CD=N (PRO) ideal from 1.474 to 1.474 actual= 1.475, sigma from 0.014 to 0.014 Angs Fix up angle B|215:C(LEU)=B|216:N(PRO)=B|216:CA(PRO) ideal from 119.3 to 127.0 actual= 131.6, sigma from 1.5 to 2.4 Degs Fix up angle B|215:C(LEU)=B|216:N(PRO)=B|216:CD(PRO) ideal from 128.4 to 120.6 actual= 118.7, sigma from 2.1 to 2.2 Degs Fix up angle B|216: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 B|216:CB=CA=C (PRO) ideal from 111.7 to 112.0 actual= 112.1, sigma from 2.1 to 2.5 Degs Fix up angle B|216:CA=CB=CG (PRO) ideal from 104.8 to 104.0 actual= 106.4, sigma from 1.9 to 1.9 Degs Fix up angle B|216:CB=CG=CD (PRO) ideal from 106.5 to 105.4 actual= 106.9, sigma from 3.9 to 2.3 Degs Fix up angle B|216:CG=CD=N (PRO) ideal from 103.2 to 103.8 actual= 103.2, sigma from 1.5 to 1.2 Degs Fix up angle B|216:CA=N=CD (PRO) ideal from 111.7 to 111.5 actual= 109.7, 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 = 7.205221E+05 rms gradient= 39.1798 X-ray contribution to function value = 6.566257E+05 Geometry contribution (inc ncs) = 63896.4 Geometry function summary term number weight rms GooF function fn/numb ================================================================================================ BOND bond lengths (angs) 4712 2.000 0.0104 0.529 2633.19 0.559 ANGL bond angles (degs) 6399 2.000 1.25 0.778 7739.23 1.209 TORS split-harmonic tors 1044 0.000 22.53 1.438 0.00 0.000 SINTOR sinusoidal tors 1044 2.000 22.53 2991.06 2.865 TRIG.onal planes (angs) 110 2.000 0.0074 0.372 30.40 0.276 PLAN general plane (angs) 665 5.000 0.0155 0.776 2001.40 3.010 BCORrelations (angs*2) 4712 20.000 1.571 0.268 6782.71 1.439 CONT (bad contacts) 0 5.000 0.00 IDEAL(ideal-dist contact) 5064 4.000 30671.96 CHIRAL (gelly semiharmon) 584 5.000 6.48 SIM similarity restraint for NCS and/or TARGET 11039.90 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 2.89 degs - monitor only WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: WARNING: 2 bond angles. Worst is 5.5 sigs 126.98 degs B|104:CD1=CG=CD2 (LEU) WARNING: 1 idealD contacts. Worst 5.0 sigs 2.39 Angs B|185:C=CG2 (THR) Weighted rms 0.0104 1.246 (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= 2.387 std= 3.390 sigma= 0.200 abs(Delta/sigma)= 5.013 ats B|185:C (THR) B|185:CG2 (THR) 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 7.205221E+05 6.566257E+05 63896.4 39.1798 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 7.202588E+05 6.565978E+05 63661.0 32.7950 9.967750E-04 0.0175744 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0006 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 002 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 2 7.199694E+05 6.565380E+05 63431.4 34.8536 0.00287978 0.0486427 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0007 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 003 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 3 7.198087E+05 6.564805E+05 63328.2 50.1318 0.00472832 0.0659398 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0008 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 004 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 4 7.196447E+05 6.564616E+05 63183.0 27.3450 0.00522508 0.0689162 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0009 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 005 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 5 7.194738E+05 6.564188E+05 63055.1 23.5265 0.00648827 0.0865958 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0010 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 006 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 6 7.193584E+05 6.563838E+05 62974.6 24.8119 0.00748340 0.102624 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0011 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 007 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 7 7.191681E+05 6.562633E+05 62904.8 60.6548 0.0111931 0.168552 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0012 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 008 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 8 7.189881E+05 6.561981E+05 62790.0 31.8712 0.0134855 0.207530 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0013 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 009 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 9 7.188950E+05 6.562019E+05 62693.1 20.3924 0.0129679 0.200383 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0014 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 010 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 10 7.187440E+05 6.561622E+05 62581.8 20.3826 0.0136604 0.213130 Opttag_D Writing pdb file to gelly_output_iter000010.pdb Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0015 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 011 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 11 7.185935E+05 6.560893E+05 62504.2 26.7796 0.0157195 0.244677 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0016 (explanation) 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 7.184851E+05 6.560086E+05 62476.5 42.2621 0.0183590 0.281578 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 7.183237E+05 6.559269E+05 62396.8 23.6517 0.0215927 0.325767 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 7.181871E+05 6.558700E+05 62317.1 21.2742 0.0239681 0.354860 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 7.180186E+05 6.558054E+05 62213.1 30.3089 0.0267163 0.390530 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 7.178918E+05 6.557422E+05 62149.6 46.4441 0.0298609 0.428108 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 7.177257E+05 6.557421E+05 61983.5 27.3533 0.0294275 0.419529 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 7.175858E+05 6.557480E+05 61837.8 20.8269 0.0286239 0.430481 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 7.174777E+05 6.557174E+05 61760.3 25.2441 0.0300867 0.477815 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 7.173878E+05 6.556850E+05 61702.8 38.4448 0.0313269 0.522583 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) 4712 2.000 0.0102 0.521 2555.80 0.542 ANGL bond angles (degs) 6399 2.000 1.23 0.767 7534.10 1.177 TORS split-harmonic tors 1044 0.000 22.55 1.440 0.00 0.000 SINTOR sinusoidal tors 1044 2.000 22.55 2989.58 2.864 TRIG.onal planes (angs) 110 2.000 0.0076 0.379 31.58 0.287 PLAN general plane (angs) 665 5.000 0.0152 0.762 1928.33 2.900 BCORrelations (angs*2) 4712 20.000 1.567 0.268 6749.21 1.432 CONT (bad contacts) 0 5.000 0.00 IDEAL(ideal-dist contact) 5057 4.000 30061.84 CHIRAL (gelly semiharmon) 584 5.000 6.79 SIM similarity restraint for NCS and/or TARGET 9845.60 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 2.88 degs - monitor only WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: WARNING: 1 bond angles. Worst is 5.4 sigs 135.20 degs B|155:C(TRP)=B|156:N(ASP)=B|156:CA(ASP) Weighted rms 0.0102 1.230 (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 terminationStatistics 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.