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: 21018 Number of rejected reflexions: 856 Reflexions in test set: 1669 (explanation) Reflexions in working set: 19349 (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 = 0.15726E+02 B = -13.855 Setting starting scale K to value from Wilson scaling: 15.72619 Setting starting scale B to value from Wilson scaling: -13.85451Cycle 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)
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: -autoncs -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 0.0 -----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 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 2109 atoms Have defined 14 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 set: 'ncsautoXcld' has 0 atoms in 0 residues - user specified set: 'ncsautoABset' has 2109 atoms in 281 residues - user specified Interpreting CONSTANT cards: =====CONSTANT B =====CONSTANT OCC Have found and interpreted 2 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 = 4217 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 Have a total of 2 COMBINE and/or NOTE BUSTER_COMBINE cards in TNT input There are no NOTE BUSTER_COMBINE_RES cards to be found in the TNT card input COMBINE groups of type XYZ use rotation method routines from: Grassia, F. S. (1998) "Practical parameterization of rotations using the exponential map" Journal of Graphics Tools, 3:29-48. http://www.acm.org/jgt/papers/Grassia98/ Interpreting COMBINE cards: =====COMBINE XYZ A|* =====COMBINE XYZ B|* Have 2 COMBINE groups of type XYZ xyz combine group number 1 has 2109 atoms in it: Residue A|7 THR N CA C O CB OG1 Residue A|8 SER N CA C O CB OG Residue A|9 ARG N CA C O CB CG CD Residue A|10 PRO N CA C O CB CG Residue A|11 PRO N CA C O CB CG Residue A|12 LEU N CA C O CB CG CD1 CD2 Residue A|13 GLU N ....... (output limited to first 40 atoms '-verbose 4' for longer report) xyz combine group number 2 has 2108 atoms in it: Residue B|7 THR CA C O CB OG1 Residue B|8 SER N CA C O CB OG Residue B|9 ARG N CA C O CB CG CD Residue B|10 PRO N CA C O CB CG Residue B|11 PRO N CA C O CB CG Residue B|12 LEU N CA C O CB CG CD1 CD2 Residue B|13 GLU N CA ....... (output limited to first 40 atoms '-verbose 4' for longer report) Do not have any COMBINE groups of type B Do not have any COMBINE groups of type OCC Number of atoms with fixed/combined xyz = 4217 Number of atoms with fixed/combined B = 4217 Number of atoms with fixed/combined OCC = 4217 Number of atoms with fixed/combined BIJ = 4217 cf total number of atoms = 4217 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= 2109 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 0.001 ----- Overall RMSD,XYZ for the SIM group is 0.001 Angstroms Pairwise rms deviation of [individual B's minus their set/chain average] in Angs**2 A B Bavg A ----- ----- 20.00 B 0.00 ----- 20.00 Overall RMSD,B for the SIM group is 0.000 Angs**2 The number of common atoms for the above fits: A B A ----- ----- B 2108 ----- (compared to the template set that has 2109 atoms in it) List of atoms that are absent in one or more chains for this group: A B N 7 + - (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 -0.999568 -0.029023 -0.004737 0.029055 -0.999554 -0.006894 -0.004535 -0.007029 0.999965 121.520 255.945 -35.401 reverse transforms TRANS_BA -0.999568 0.029055 -0.004535 -0.029023 -0.999554 -0.007029 -0.004737 -0.006894 0.999965 113.870 259.109 37.739 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 24359 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: Residues pruned out by function/max condition: Total number of residues pruned out is 0 out of 561 participating Number of LSSR restraints pruned out is 0 this is 0.0% 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 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 1.6 after pruning 1.6 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=100.00% average DeltaD of subset 0.000 Angs Histogram of LSSR deltaD distribution ncs_histogram.mtv No 'NOTE BUSTER_TLS_SET' cards found - so no TLS constraints will be used Numb parameters added for rigid body rotation/translation= 12 Number of parameters to describe molecular conformation = 12 Number of free parameters to be adjusted in refinement = 12 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 0.000 0 0.000 0.000 0.000 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 = 4.031350E+05 rms gradient= 3685.00 X-ray contribution to function value = 2.741764E+05 Geometry contribution (inc ncs) = 1.289585E+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 0.000 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 1.62 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 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 100 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 4.031350E+05 2.741764E+05 1.289585E+05 3685.00 1.986003E-16 1.776357E-15 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0004 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 001 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 1 4.025817E+05 2.740888E+05 1.284929E+05 3359.65 0.0311868 0.0503035 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0005 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 002 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 2 4.001083E+05 2.749964E+05 1.251119E+05 1164.35 0.377399 0.698268 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0006 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 003 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 3 3.997908E+05 2.748398E+05 1.249511E+05 719.457 0.352214 0.686668 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0007 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 004 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 4 3.994318E+05 2.748681E+05 1.245637E+05 567.204 0.352575 0.776738 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0008 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 005 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 5 3.991609E+05 2.752317E+05 1.239292E+05 460.496 0.408150 0.979634 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0009 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 006 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 6 3.990874E+05 2.754694E+05 1.236180E+05 226.285 0.448487 1.14492 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0010 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 007 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 7 3.990741E+05 2.754536E+05 1.236205E+05 144.849 0.450436 1.11862 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0011 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 008 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 8 3.990697E+05 2.754551E+05 1.236146E+05 33.5594 0.449404 1.11794 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0012 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 009 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 9 3.990691E+05 2.754658E+05 1.236033E+05 27.8057 0.450765 1.12090 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0013 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 010 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 10 3.990677E+05 2.754877E+05 1.235800E+05 30.6357 0.453619 1.12514 Opttag_D Writing pdb file to gelly_output_iter000010.pdb Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0014 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 011 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 11 3.990670E+05 2.754793E+05 1.235877E+05 17.2721 0.452553 1.12142 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0015 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 012 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 12 3.990670E+05 2.754788E+05 1.235882E+05 22.6479 0.452666 1.11858 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0016 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 013 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 13 3.990669E+05 2.754768E+05 1.235901E+05 3.81361 0.452311 1.11904 Opttag_D Geometry Restraint Deviations SCREEN Information MaxLik Scaling Cycle 0017 (explanation) Wilson plot Statistics in resolution bins after refinement cycle 014 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init 14 3.990669E+05 2.754763E+05 1.235906E+05 3.17372 0.452254 1.11904 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) 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 0.000 0.00 IDEAL(ideal-dist contact) 4546 4.000 51483.62 CHIRAL (gelly semiharmon) 557 5.000 15276.32 SIM similarity restraint for NCS and/or TARGET 1.62 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: 47 idealD contacts. Worst 14.2 sigs 0.86 Angs A|89:CA=C (GLU) 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!) 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.