Please reference use of the software as:
Version: 2.13.0 for linux64-ifort made on Oct 28 2013 at 08:44:09
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: 19421 Number of accepted reflexions: 19390 Number of rejected reflexions: 31 Reflexions in test set: 1031 (explanation) Reflexions in working set: 18359 (explanation)
1. Generating initial model
2.10 * Shannon sampling rate. NX NY NZ: 120 120 480 Effective Shannon rates are: 2.40 2.40 2.42 Allocated BUFFER of size: 26.807 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 1.05327) ... 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 = 0.93078E+00 B = -13.889 Setting starting scale K to value from Wilson scaling: 0.93078 Setting starting scale B to value from Wilson scaling: -13.88898Cycle 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 = 3.1444 Å2 to all atoms in fragment Added B = 3.1444 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 Aug 16 2013 13:15:31 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: -forcefield I0G \ -autoncs -screen \ 100 -screen_sigma \ 3.0 Setting up tnt routines including license check: TNT Stereochemistry Program Version: 5.25.0.0 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 3568 atoms from TNT to gelly's store The TNT WEIGHT cards used this run: -----WEIGHT BOND 2.0 -----WEIGHT ANGLE 2.0 -----WEIGHT IMPROPER 0.0 -----WEIGHT TORSION 2.0 -----WEIGHT PSEUDO 0.0 -----WEIGHT TRIGONAL 2.0 -----WEIGHT PLANE 5.0 -----WEIGHT CONTACT 5.0 -----WEIGHT BCORREL 20.0 -----WEIGHT CHIRAL 5.0 -----WEIGHT NCS 50.0 -----WEIGHT IDEAL 4.0 -----WEIGHT RFACTOR 4 Dictionary versions picked up from NOTE BUSTER_RESTRAINT_DICT cards as: ------ protgeo_eh99.dat (V1.16) 20131014 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 (V1.14) 20120418 COLLECTION OF NON-STANDARD AMINO ACIDS, MAINLY EH91 WITHOUT IDEAL DISTANCE INFO ------ nuclgeo.dat (V1.27) 20120611 ------ bcorrel.dat (V1.15) 20080423 ------ contact.dat (V1.23) 20121002 ------ idealdist_contact.dat (V1.11) 20121011 IDEAL-DISTANCE CONTACT TERM DATA AS USED IN PROLSQ. VALUES USED HERE ARE BASED ON THE REFMAC 5.5 IMPLEMENTATION. ------ restraints for I0G (_3AS,4R,9BR_-4-_4-HYDROXYPHENYL_-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA_C_CHROMEN-8-OL) from cif dictionary I0G.grade_PDB_ligand.cif using refmacdict2tnt revision 1.40; generated by GRADE 1.2.3 from mol2 file /tmp/filep4kTkr.mol2 using mogul+qm ------ assume.dat (V1.10) 20110113 Have picked up spacegroup name for pdb output as 'P 61 ' 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 . 100% 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 Have command line argument: '-forcefield I0G' so will setup Force Field calculation for ligand. Please note that -forcefield shares code with QM. three-letter code decoded to be ='I0G' charge set to= 0 Setting up QM calculation by producing .Gelly type cards for internal use: NOTE BUSTER_QM_HELPER $BDG_home/scripts/qm-mm-helpers/forcefield.pl # the helper program used must be on path or full path spec NOTE BUSTER_QM_METHOD AUTO # the method/basis set to be used (helper must understand) NOTE BUSTER_QM_WEIGHT 16.000 # qm weight NOTE BUSTER_QM_MAXDISP 100000.000 # maximum displacement from previous position to protect QM. NOTE BUSTER_SET QM01 = { A|1 } # residue type I0G NOTE BUSTER_QM_CHARGE_01 0 # charge of I0G NOTE BUSTER_QM_MULTIP_01 1 # multiplicity (normally one) NOTE BUSTER_QM_WRESTR_01 0.0 # weight for conventional restraints involving only QM01 # atoms, normally set to 0.0 to turn off completely NOTE BUSTER_SET QM02 = { B|1 } # residue type I0G NOTE BUSTER_QM_CHARGE_02 0 # charge of I0G NOTE BUSTER_QM_MULTIP_02 1 # multiplicity (normally one) NOTE BUSTER_QM_WRESTR_02 0.0 # weight for conventional restraints involving only QM02 # atoms, normally set to 0.0 to turn off completely Setting up BUSTER_SET groups Have found 37 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 17 atoms =====NOTE BUSTER_SET ncsautoABset = Chain_B \ ncsautoXcld --> set 'ncsautoABset' now has 1781 atoms =====NOTE BUSTER_SET QM01 = { A|1 } --> set 'QM01' now has 39 atoms =====NOTE BUSTER_SET QM02 = { B|1 } --> set 'QM02' now has 39 atoms Have defined 16 sets: set: 'All' has 3568 atoms in 462 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 3473 atoms in 443 residues - automatically defined set: 'Chain_A' has 1778 atoms in 230 residues - automatically defined set: 'Chain_B' has 1790 atoms in 232 residues - automatically defined set: 'Water' has 17 atoms in 17 residues - defined by dictionary file set: 'StdProtein' has 3473 atoms in 443 residues - defined by dictionary file set: 'Protein' has 3473 atoms in 443 residues - defined by dictionary file set: 'Back' has 1772 atoms in 443 residues - defined by dictionary file set: 'Side' has 1701 atoms in 429 residues - defined by dictionary file set: 'Other' has 78 atoms in 2 residues - defined by dictionary file set: 'ncsautoXcld' has 17 atoms in 17 residues - user specified set: 'ncsautoABset' has 1781 atoms in 223 residues - user specified set: 'QM01' has 39 atoms in 1 residues - user specified set: 'QM02' has 39 atoms in 1 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 = 3568 Before any COMBINE - Number of atoms with fixed BIJ = 3568 cf total number of atoms = 3568 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 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 A Number of atoms in template set= 1781 Number of related chains (other than template) in SIM set= 1 List of chains to be restrained (excluding template)= A Pairwise RMSD, XYZ in Angstroms, for SIM group: ncsautoAB B A B ----- ----- A 0.507 ----- Overall RMSD,XYZ for the SIM group is 0.507 Angstroms Pairwise rms deviation of [individual B's minus their set/chain average] in Angs**2 B A Bavg B ----- ----- 56.72 A 2.82 ----- 56.41 Overall RMSD,B for the SIM group is 2.815 Angs**2 The number of common atoms for the above fits: B A B ----- ----- A 1770 ----- (compared to the template set that has 1781 atoms in it) List of atoms that are absent in one or more chains for this group: B A N 260 + - CA 260 + - C 260 + - O 260 + - CB 260 + - CG 260 + - CD1 260 + - CD2 260 + - CG 261 + - OD1 261 + - OD2 261 + - (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_BA -0.500942 0.865481 -0.000147 0.865480 0.500942 -0.000792 -0.000611 -0.000524 -1.000000 94.893 -54.647 117.095 reverse transforms TRANS_AB -0.500942 0.865480 -0.000611 0.865481 0.500942 -0.000524 -0.000147 -0.000792 -1.000000 94.903 -54.692 117.066 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 22948 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|298 B|298 Residues pruned out by function/max condition: A|267 A|282 A|329 A|364 A|428 B|267 B|282 B|329 B|364 B|428 Total number of residues pruned out is 12 out of 444 participating Number of LSSR restraints pruned out is 1476 this is 6.4% 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 + { B|267 B|282 B|298 B|329 B|364 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoXcld = ncsautoXcld + { B|428 } # card added - produced by -autoncs NOTE BUSTER_SET ncsautoABset = Chain_B \ ncsautoXcld # card added - produced by -autoncs NOTE BUSTER_SIM_DEFINE ncsautoAB ncsautoABset A # card added - produced by -autoncs NOTE BUSTER_SIM_RESTRAIN_LSSR ncsautoAB 2.000 # card added - produced by -autoncs LSSR function contribution before pruning 56224.1 after pruning 43187.5 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= 98.34% average DeltaD of subset 0.073 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 = 14272 Number of free parameters to be adjusted in refinement = 14272 No command line argument '-tnt_fn' so will use gelly to do geometry function calculations No standard contact distance given for a contact between H and H (setting to default: 1.50 +- 0.10 Angstroms) The names of the offending atoms are B|1:HO20 B|1:H18 Getting symmetry operators from TNT. gelly will classify symmetry using pdb-like convention: SYMOP SYMMETRY NNNMMM OPERATOR 1555 X,Y,Z 2555 -Y,X-Y,1/3+Z 3555 -X+Y,-X,2/3+Z 4555 -X,-Y,1/2+Z 5555 Y,-X+Y,5/6+Z 6555 X-Y,X,1/6+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 31 (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 3617 2503.925 2503.925 0.000 ANGL 2.000 4921 6083.072 6083.072 0.000 IMPR 0.000 0 0.000 0.000 0.000 TORS 2.000 1283 2059.669 2059.669 0.000 TRIG 2.000 71 1.317 1.317 0.000 PLAN 5.000 541 846.510 846.510 0.000 CONT 5.000 0 241.767 0.000 241.767 BCOR 20.000 3533 15912.584 15912.584 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|1:C4(I0G) A|1:C2(I0G) add a default BCOR for bond A|1:C4(I0G) A|1:C23(I0G) add a default BCOR for bond A|1:C4(I0G) A|1:C6(I0G) add a default BCOR for bond A|1:C4(I0G) A|1:H4(I0G) add a default BCOR for bond A|1:C6(I0G) A|1:C12(I0G) add a default BCOR for bond A|1:C6(I0G) A|1:C7(I0G) add a default BCOR for bond A|1:C7(I0G) A|1:C8(I0G) add a default BCOR for bond A|1:C7(I0G) A|1:H7(I0G) add a default BCOR for bond A|1:C8(I0G) A|1:C10(I0G) add a default BCOR for bond A|1:C8(I0G) A|1:O9(I0G) add a default BCOR for bond A|1:C10(I0G) A|1:C11(I0G) add a default BCOR for bond A|1:C10(I0G) A|1:H10(I0G) add a default BCOR for bond A|1:C17(I0G) A|1:C16(I0G) add a default BCOR for bond A|1:C17(I0G) A|1:C18(I0G) add a default BCOR for bond A|1:C17(I0G) A|1:H17(I0G) add a default BCOR for bond A|1:C21(I0G) A|1:C19(I0G) add a default BCOR for bond A|1:C21(I0G) A|1:C22(I0G) add a default BCOR for bond A|1:C21(I0G) A|1:H21(I0G) add a default BCOR for bond A|1:C22(I0G) A|1:C16(I0G) add a default BCOR for bond A|1:C22(I0G) A|1:H22(I0G) add a default BCOR for bond A|1:C24(I0G) A|1:C1(I0G) add a default BCOR for bond A|1:C24(I0G) A|1:C23(I0G) add a default BCOR for bond A|1:C24(I0G) A|1:H241(I0G) add a default BCOR for bond A|1:C24(I0G) A|1:H242(I0G) add a default BCOR for bond A|1:C1(I0G) A|1:C2(I0G) add a default BCOR for bond A|1:C1(I0G) A|1:H11A(I0G) add a default BCOR for bond A|1:C1(I0G) A|1:H12(I0G) add a default BCOR for bond A|1:C2(I0G) A|1:C14(I0G) add a default BCOR for bond A|1:C2(I0G) A|1:H2(I0G) add a default BCOR for bond A|1:O9(I0G) A|1:HO9(I0G) add a default BCOR for bond A|1:C11(I0G) A|1:C12(I0G) add a default BCOR for bond A|1:C11(I0G) A|1:H11(I0G) add a default BCOR for bond A|1:C12(I0G) A|1:O13(I0G) add a default BCOR for bond A|1:O13(I0G) A|1:C14(I0G) add a default BCOR for bond A|1:C14(I0G) A|1:C16(I0G) add a default BCOR for bond A|1:C14(I0G) A|1:H14(I0G) add a default BCOR for bond A|1:C18(I0G) A|1:C19(I0G) add a default BCOR for bond A|1:C18(I0G) A|1:H18(I0G) add a default BCOR for bond A|1:C19(I0G) A|1:O20(I0G) add a default BCOR for bond A|1:O20(I0G) A|1:HO20(I0G) only first 40 added listed here Have added a total of 84 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 435 Number of other torsion is 848 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 Weight for ideal-distance contact term= 4.000 Have 'NOTE BUSTER_QM_HELPER'. Will setup quantum chemical calculation qmcommand= $BDG_home/scripts/qm-mm-helpers/forcefield.pl Have 'NOTE BUSTER_QM_METHOD'. Method/basis to be used AUTO Have read value from 'NOTE BUSTER_QM_WEIGHT' card = 16.000 Have read value from 'NOTE BUSTER_QM_MAXDISP' card = 100000.000 Factor to get QM kJ/mol onto sigma scale= 0.8045 QM_WEIGHT= 16.0000 (can overide by 'NOTE BUSTER_QM_WEIGHT' value card) Have found 2 QM.. type sets Number of atoms in QM set 01 is 39 including 18 hydrogens atoms (to get a pdb file containing just atoms from the QM set rerun with '-qm_wpdb' option) NOTE BUSTER_QM_CHARGE_01 sets charge= 0 NOTE BUSTER_QM_MULTIP_01 sets multip= 1 NOTE BUSTER_QM_WRESTR_01 sets wrestr= 0.000 Number of atoms in QM set 02 is 39 including 18 hydrogens atoms (to get a pdb file containing just atoms from the QM set rerun with '-qm_wpdb' option) NOTE BUSTER_QM_CHARGE_02 sets charge= 0 NOTE BUSTER_QM_MULTIP_02 sets multip= 1 NOTE BUSTER_QM_WRESTR_02 sets wrestr= 0.000 first QM calculation of energy/gradient Have 2 qm sets writing out coords for set 1 to 'gelly_coords_for_qmhelper.crdin' writing out coords for set 1 to 'gelly_coords_for_helper.xyz' writing out coords for set 1 to 'gelly_coords_for_helper.xyz_plus_bond' setting up GEOMBONDREC_TYPE_HASH* so as to be able to map type cif bond type "single" to integer GBOND_TYPE=1 etc. using default GEOMBONDREC_TYPE_HASH_STR='SING* 1 DOUB* 2 TRIP* 3 AROM* 4 DELO* 4 METAL* 5' to override default use a NOTE BUSTER_GEOMBONDREC_TYPE_HASH_STR gelly card using SYSTEM to invoke unix command: bash -c "$BDG_home/scripts/qm-mm-helpers/forcefield.pl 0 1 'AUTO' &> gelly_qm_helper.log" QM_HELPER_LOG: forcefield.pl invoking OpenEye Helper with /mnt/scratch_fs1/osmart/autobuster/Server/scripts/qm-mm-helpers/OpenEye.pl 0 1 AUTO QM_HELPER_LOG: QM_HELPER_LOG: gelly helper script to run OpenEye helpers for force field or QM energy/gradient calculation QM_HELPER_LOG: Please obtain helpers for OpenEye http://www.eyesopen.com/ QM_HELPER_LOG: helper script location /mnt/scratch_fs1/osmart/autobuster/Server/scripts/qm-mm-helpers/OpenEye.pl QM_HELPER_LOG: picked up charge=0 multip=1 method=AUTO from command line QM_HELPER_LOG: Open Eye executable used: /home/osmart/2013/09/OpenEyeHelper/openeye/bin//buster_helper_mmff QM_HELPER_LOG: :jGf: QM_HELPER_LOG: :jGDDDDf: QM_HELPER_LOG: ,fDDDGjLDDDf, BUSTER HELPER MMFF QM_HELPER_LOG: ,fDDLt: :iLDDL; QM_HELPER_LOG: ;fDLt: :tfDG; QM_HELPER_LOG: ,jft: ,ijfffji, :iff QM_HELPER_LOG: .jGDDDDDDDDDGt. QM_HELPER_LOG: ;GDDGt:''':tDDDG, QM_HELPER_LOG: .DDDG: :GDDG. QM_HELPER_LOG: ;DDDj tDDDi QM_HELPER_LOG: ,DDDf fDDD, Copyright (c) 2013 QM_HELPER_LOG: LDDDt. .fDDDj OpenEye Scientific Software, Inc. QM_HELPER_LOG: .tDDDDfjtjfDDDGt QM_HELPER_LOG: :ifGDDDDDGfi. Version: 2.3.0.4 QM_HELPER_LOG: .:::. Built: 20130710 QM_HELPER_LOG: ...................... OEChem version: 1.9.2 20130710 QM_HELPER_LOG: DDDDDDDDDDDDDDDDDDDDDD Platform: Ubuntu-12.04-g++4.6-x64 QM_HELPER_LOG: DDDDDDDDDDDDDDDDDDDDDD QM_HELPER_LOG: QM_HELPER_LOG: QM_HELPER_LOG: QM_HELPER_LOG: Input ISM: c1cc(ccc1C2C3CCCC3c4cc(ccc4O2)O)O QM energy for QMset 1 picked up as 316.47988 writing out coords for set 2 to 'gelly_coords_for_qmhelper.crdin' writing out coords for set 2 to 'gelly_coords_for_helper.xyz' writing out coords for set 2 to 'gelly_coords_for_helper.xyz_plus_bond' using SYSTEM to invoke unix command: bash -c "$BDG_home/scripts/qm-mm-helpers/forcefield.pl 0 1 'AUTO' &> gelly_qm_helper.log" QM_HELPER_LOG: forcefield.pl invoking OpenEye Helper with /mnt/scratch_fs1/osmart/autobuster/Server/scripts/qm-mm-helpers/OpenEye.pl 0 1 AUTO QM_HELPER_LOG: QM_HELPER_LOG: gelly helper script to run OpenEye helpers for force field or QM energy/gradient calculation QM_HELPER_LOG: Please obtain helpers for OpenEye http://www.eyesopen.com/ QM_HELPER_LOG: helper script location /mnt/scratch_fs1/osmart/autobuster/Server/scripts/qm-mm-helpers/OpenEye.pl QM_HELPER_LOG: picked up charge=0 multip=1 method=AUTO from command line QM_HELPER_LOG: Open Eye executable used: /home/osmart/2013/09/OpenEyeHelper/openeye/bin//buster_helper_mmff QM_HELPER_LOG: :jGf: QM_HELPER_LOG: :jGDDDDf: QM_HELPER_LOG: ,fDDDGjLDDDf, BUSTER HELPER MMFF QM_HELPER_LOG: ,fDDLt: :iLDDL; QM_HELPER_LOG: ;fDLt: :tfDG; QM_HELPER_LOG: ,jft: ,ijfffji, :iff QM_HELPER_LOG: .jGDDDDDDDDDGt. QM_HELPER_LOG: ;GDDGt:''':tDDDG, QM_HELPER_LOG: .DDDG: :GDDG. QM_HELPER_LOG: ;DDDj tDDDi QM_HELPER_LOG: ,DDDf fDDD, Copyright (c) 2013 QM_HELPER_LOG: LDDDt. .fDDDj OpenEye Scientific Software, Inc. QM_HELPER_LOG: .tDDDDfjtjfDDDGt QM_HELPER_LOG: :ifGDDDDDGfi. Version: 2.3.0.4 QM_HELPER_LOG: .:::. Built: 20130710 QM_HELPER_LOG: ...................... OEChem version: 1.9.2 20130710 QM_HELPER_LOG: DDDDDDDDDDDDDDDDDDDDDD Platform: Ubuntu-12.04-g++4.6-x64 QM_HELPER_LOG: DDDDDDDDDDDDDDDDDDDDDD QM_HELPER_LOG: QM_HELPER_LOG: QM_HELPER_LOG: QM_HELPER_LOG: Input ISM: c1cc(ccc1C2C3CCCC3c4cc(ccc4O2)O)O QM energy for QMset 2 picked up as 321.58912 Zero weight (or re-weight) conventional restraints involving QM atoms all from the same QM set Term number of re-weighted restraint for each QM set =========+========+========+========+========+ BOND 42 42 ANGL 75 75 TORS 12 12 TRIG 0 0 PLAN 25 25 Information for buster-report to pick up and to be included in output PDB file: QMFFINFO I0G A 1, represented by force field, Program OpenEye Scientific Software, Inc. helper Version: 2.3.0.4 (20130710), Method MMFF94s, weight 16.0 QMFFINFO I0G B 1, represented by force field, Program OpenEye Scientific Software, Inc. helper Version: 2.3.0.4 (20130710), Method MMFF94s, weight 16.0 No ligand-(fixed protein) contact term will be used MaxLik Scaling Cycle 0002 (explanation) Initial functional value = 5.089202E+05 rms gradient= 322.149 X-ray contribution to function value = 3.888182E+05 Geometry contribution (inc ncs) = 1.201020E+05 Geometry function summary term number weight rms GooF function fn/numb ================================================================================================ BOND bond lengths (angs) 3533 2.000 0.0103 0.506 1806.11 0.511 ANGL bond angles (degs) 4771 2.000 1.36 0.787 5915.82 1.240 TORS split-harmonic tors 824 0.000 17.35 1.118 0.00 0.000 SINTOR sinusoidal tors 824 2.000 17.35 1513.71 1.837 TRIG.onal planes (angs) 71 2.000 0.0019 0.096 1.32 0.019 PLAN general plane (angs) 491 5.000 0.0115 0.574 809.74 1.649 BCORrelations (angs*2) 3617 20.000 2.689 0.469 15931.20 4.405 CONT (bad contacts) 0 5.000 0.00 IDEAL(ideal-dist contact) 4522 4.000 42610.65 CHIRAL (gelly semiharmon) 465 5.000 112.71 SIM similarity restraint for NCS and/or TARGET 43187.50 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 QM quantum chemical function/sum of energies 8213.22 638.07 QM energy of each set in kJ/mol: 316.48 321.59 Peptide omega torsion angles 1.22 degs - monitor only WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: WARNING: 7 bond angles. Worst is 7.9 sigs 131.72 degs A|428:CB=CG=ND1 (HIS) Weighted rms 0.0103 1.359 (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= 2.880 std= 3.860 sigma= 0.200 abs(Delta/sigma)= 4.902 ats A|386:CB (ARG) B|410:CE (MET) 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 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 5.089202E+05 3.888182E+05 1.201020E+05 322.149 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 4.974682E+05 3.888985E+05 1.085697E+05 225.393 0.00447979 0.0322309 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 4.843706E+05 3.891164E+05 95254.2 309.181 0.0169324 0.0990540 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 4.791869E+05 3.892848E+05 89902.1 389.368 0.0280208 0.129990 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 4.734945E+05 3.892124E+05 84282.1 198.477 0.0283185 0.119547 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 4.679128E+05 3.891727E+05 78740.2 158.513 0.0340845 0.132718 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 4.638967E+05 3.892050E+05 74691.7 172.351 0.0413976 0.170007 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 4.578417E+05 3.892901E+05 68551.6 181.553 0.0553824 0.229924 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0012 (explanation)
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 4.558134E+05 3.893008E+05 66512.6 148.656 0.0603574 0.243198 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 4.540515E+05 3.893037E+05 64747.8 96.5021 0.0627247 0.245742 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 4.522330E+05 3.892847E+05 62948.3 116.055 0.0656131 0.255894 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 4.506327E+05 3.892469E+05 61385.8 135.064 0.0694380 0.280843 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 4.488420E+05 3.892465E+05 59595.5 99.9100 0.0764703 0.326889 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 4.476496E+05 3.892257E+05 58423.8 80.0633 0.0789699 0.335712 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 4.464387E+05 3.892157E+05 57223.0 105.025 0.0822128 0.337258 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 4.453848E+05 3.892368E+05 56147.9 110.347 0.0858009 0.369810 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 4.441798E+05 3.892669E+05 54912.9 69.2197 0.0899606 0.409305 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 4.430795E+05 3.892922E+05 53787.3 66.1835 0.0944218 0.442564 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 4.422801E+05 3.893021E+05 52977.9 114.849 0.0992446 0.470279 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 4.414596E+05 3.892917E+05 52168.0 83.0304 0.102395 0.481469 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 4.407780E+05 3.892640E+05 51514.0 57.5286 0.103993 0.478924 Opttag_D
Writing pdb file to gelly_output_iter000020.pdb
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0026 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 021 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
21 4.400543E+05 3.892406E+05 50813.7 60.4859 0.106832 0.475987 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0027 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 022 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
22 4.395063E+05 3.892452E+05 50261.2 75.0614 0.110218 0.478504 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0028 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 023 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
23 4.388877E+05 3.892705E+05 49617.2 64.2816 0.114078 0.509091 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0029 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 024 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
24 4.383837E+05 3.893174E+05 49066.4 86.0435 0.118746 0.547090 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0030 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 025 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
25 4.379112E+05 3.893374E+05 48573.9 52.0650 0.120294 0.573998 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0031 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 026 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
26 4.375575E+05 3.893431E+05 48214.4 55.8671 0.121506 0.600962 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0032 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 027 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
27 4.368425E+05 3.893528E+05 47489.7 62.5742 0.125573 0.688854 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0033 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 028 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
28 4.360604E+05 3.893978E+05 46662.6 94.8669 0.134126 0.885102 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0034 (explanation)
MaxLik Scaling Cycle 0035 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 029 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
29 4.357212E+05 3.893820E+05 46339.2 68.7729 0.135237 0.931635 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0036 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 030 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
30 4.352630E+05 3.892870E+05 45976.0 39.9311 0.130716 0.896860 Opttag_D
Writing pdb file to gelly_output_iter000030.pdb
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0037 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 031 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
31 4.348941E+05 3.892963E+05 45597.7 34.8725 0.133035 0.943734 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0038 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 032 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
32 4.346291E+05 3.892794E+05 45349.7 43.8148 0.134052 0.971108 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0039 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 033 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
33 4.343845E+05 3.892777E+05 45106.8 55.5341 0.136535 1.00835 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0040 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 034 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
34 4.341524E+05 3.892928E+05 44859.6 32.3364 0.138517 1.02263 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0041 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 035 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
35 4.339675E+05 3.892893E+05 44678.2 34.2481 0.139666 1.02046 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0042 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 036 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
36 4.337188E+05 3.892942E+05 44424.6 41.0567 0.142105 1.01195 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0043 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 037 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
37 4.335667E+05 3.893185E+05 44248.2 93.3842 0.148293 0.985884 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0044 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 038 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
38 4.332093E+05 3.893253E+05 43884.0 36.4064 0.149693 1.00122 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0045 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 039 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
39 4.330737E+05 3.893324E+05 43741.3 25.5611 0.150602 1.00963 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0046 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 040 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
40 4.329192E+05 3.893519E+05 43567.3 32.5658 0.153084 1.01466 Opttag_D
Writing pdb file to gelly_output_iter000040.pdb
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0047 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 041 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
41 4.327002E+05 3.893831E+05 43317.1 53.5696 0.157579 1.02791 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0048 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 042 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
42 4.324921E+05 3.894132E+05 43078.9 31.8298 0.161099 1.03685 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0049 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 043 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
43 4.323029E+05 3.894340E+05 42869.0 25.8816 0.164183 1.04928 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0050 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 044 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
44 4.321725E+05 3.894476E+05 42724.9 45.8318 0.166858 1.06577 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0051 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 045 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
45 4.320186E+05 3.894561E+05 42562.5 34.5624 0.168727 1.08086 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0052 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 046 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
46 4.318229E+05 3.894632E+05 42359.7 29.3487 0.171001 1.10459 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0053 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 047 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
47 4.316205E+05 3.894747E+05 42145.8 36.3782 0.174167 1.13523 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0054 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 048 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
48 4.314351E+05 3.894996E+05 41935.5 37.7523 0.178391 1.16779 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0055 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 049 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
49 4.312754E+05 3.894939E+05 41781.6 27.2222 0.179292 1.17435 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0056 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 050 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
50 4.310842E+05 3.894917E+05 41592.5 39.2371 0.181510 1.18898 Opttag_D
Writing pdb file to gelly_output_iter000050.pdb
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0057 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 051 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
51 4.310117E+05 3.894942E+05 41517.6 50.3371 0.183347 1.20063 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0058 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 052 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
52 4.309168E+05 3.894846E+05 41432.2 26.9147 0.182851 1.19827 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0059 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 053 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
53 4.307953E+05 3.894837E+05 41311.6 23.1991 0.183845 1.20765 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0060 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 054 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
54 4.306844E+05 3.894719E+05 41212.6 30.2948 0.184846 1.21692 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0061 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 055 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
55 4.304875E+05 3.894758E+05 41011.7 31.8257 0.187771 1.23801 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0062 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 056 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
56 4.303961E+05 3.894446E+05 40951.5 93.1686 0.191063 1.26495 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0063 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 057 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
57 4.300916E+05 3.894773E+05 40614.3 28.3273 0.193954 1.27991 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0064 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 058 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
58 4.299822E+05 3.894848E+05 40497.4 21.0733 0.194113 1.27852 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0065 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 059 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
59 4.298332E+05 3.894991E+05 40334.1 25.1656 0.196517 1.29031 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0066 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 060 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
60 4.296842E+05 3.895067E+05 40177.6 49.5855 0.198989 1.30212 Opttag_D
Writing pdb file to gelly_output_iter000060.pdb
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0067 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 061 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
61 4.295267E+05 3.894907E+05 40036.1 26.1085 0.199422 1.30415 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0068 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 062 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
62 4.294289E+05 3.895059E+05 39923.0 20.6252 0.201404 1.31660 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0069 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 063 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
63 4.293580E+05 3.894806E+05 39877.4 26.4545 0.201481 1.32023 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0070 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 064 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
64 4.292773E+05 3.894767E+05 39800.6 21.8233 0.202340 1.32752 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0071 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 065 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
65 4.291519E+05 3.895226E+05 39629.3 23.7068 0.206887 1.35643 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0072 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 066 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
66 4.290319E+05 3.894395E+05 39592.3 38.5684 0.204326 1.35069 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0073 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 067 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
67 4.288941E+05 3.894552E+05 39438.9 24.9408 0.205859 1.36093 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0074 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 068 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
68 4.288038E+05 3.894603E+05 39343.5 18.1856 0.206234 1.36385 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0075 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 069 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
69 4.287376E+05 3.894418E+05 39295.8 20.0463 0.206373 1.36595 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0076 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 070 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
70 4.287068E+05 3.893991E+05 39307.7 51.7870 0.206712 1.37468 Opttag_D
Writing pdb file to gelly_output_iter000070.pdb
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0077 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 071 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
71 4.286134E+05 3.893984E+05 39215.0 16.0516 0.206985 1.37887 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0078 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 072 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
72 4.285832E+05 3.893983E+05 39184.9 15.6406 0.207603 1.38185 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0079 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 073 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
73 4.285151E+05 3.893777E+05 39137.4 22.7774 0.207778 1.38590 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0080 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 074 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
74 4.284113E+05 3.893700E+05 39041.2 24.7453 0.210572 1.40587 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0081 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 075 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
75 4.282424E+05 3.893204E+05 38922.0 44.4469 0.213857 1.43480 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0082 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 076 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
76 4.281474E+05 3.893071E+05 38840.4 45.9451 0.215436 1.44882 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0083 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 077 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
77 4.279822E+05 3.893255E+05 38656.6 22.7971 0.213415 1.43587 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0084 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 078 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
78 4.279057E+05 3.893649E+05 38540.8 26.8483 0.217295 1.46304 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0085 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 079 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
79 4.278489E+05 3.893380E+05 38510.9 15.0903 0.216129 1.45552 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0086 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 080 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
80 4.278036E+05 3.893190E+05 38484.5 14.1619 0.215299 1.45323 Opttag_D
Writing pdb file to gelly_output_iter000080.pdb
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0087 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 081 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
81 4.277743E+05 3.893135E+05 38460.8 19.9746 0.216119 1.46260 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0088 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 082 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
82 4.277472E+05 3.893127E+05 38434.5 11.7950 0.216407 1.46542 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0089 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 083 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
83 4.277215E+05 3.893143E+05 38407.2 10.5666 0.217016 1.47137 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0090 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 084 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
84 4.276925E+05 3.893086E+05 38383.9 13.2912 0.217614 1.47755 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0091 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 085 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
85 4.276451E+05 3.892918E+05 38353.3 15.1889 0.218479 1.48762 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0092 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 086 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
86 4.276359E+05 3.892569E+05 38379.1 43.0348 0.220650 1.51207 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0093 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 087 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
87 4.275459E+05 3.892457E+05 38300.2 15.2552 0.220597 1.51233 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0094 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 088 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
88 4.275029E+05 3.892356E+05 38267.3 11.6772 0.220893 1.51603 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0095 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 089 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
89 4.274418E+05 3.892138E+05 38228.0 17.3565 0.222345 1.53113 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0096 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 090 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
90 4.273656E+05 3.891947E+05 38170.9 20.4243 0.225213 1.55812 Opttag_D
Writing pdb file to gelly_output_iter000090.pdb
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0097 (explanation)
MaxLik Scaling Cycle 0098 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 091 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
91 4.273091E+05 3.891771E+05 38132.0 26.0009 0.228545 1.58885 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0099 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 092 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
92 4.272381E+05 3.891714E+05 38066.7 12.7938 0.231210 1.61304 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0100 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 093 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
93 4.271920E+05 3.891735E+05 38018.6 13.3128 0.232612 1.62569 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0101 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 094 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
94 4.271411E+05 3.891709E+05 37970.2 17.6489 0.234573 1.64326 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0102 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 095 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
95 4.270873E+05 3.891753E+05 37912.0 18.4129 0.237578 1.67085 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0103 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 096 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
96 4.270412E+05 3.891683E+05 37872.9 11.3508 0.238286 1.67702 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0104 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 097 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
97 4.270001E+05 3.891610E+05 37839.1 12.6669 0.239389 1.68776 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0105 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 098 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
98 4.269639E+05 3.891572E+05 37806.6 17.6856 0.240741 1.69934 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0106 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 099 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
99 4.269184E+05 3.891490E+05 37769.4 13.4207 0.242148 1.71110 Opttag_D
Geometry Restraint Deviations SCREEN Information
MaxLik Scaling Cycle 0107 (explanation)
Wilson plot
Statistics in resolution bins after refinement cycle 100 (explanation) :
Iters Tot_Funct Xray_Funct Geom_Funct Grms rmsD2init maxD2init
100 4.268779E+05 3.891429E+05 37735.0 10.8519 0.243651 1.72498 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) 3533 2.000 0.0085 0.413 1206.83 0.342
ANGL bond angles (degs) 4771 2.000 0.98 0.570 3104.47 0.651
TORS split-harmonic tors 824 0.000 18.63 1.200 0.00 0.000
SINTOR sinusoidal tors 824 2.000 18.63 1765.90 2.143
TRIG.onal planes (angs) 71 2.000 0.0058 0.292 12.10 0.170
PLAN general plane (angs) 491 5.000 0.0114 0.569 795.26 1.620
BCORrelations (angs*2) 3617 20.000 0.862 0.150 1635.63 0.452
CONT (bad contacts) 0 5.000 0.00
IDEAL(ideal-dist contact) 4123 4.000 20124.52
CHIRAL (gelly semiharmon) 465 5.000 39.88
SIM similarity restraint for NCS and/or TARGET 2078.56
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
QM quantum chemical function/sum of energies 6971.87 541.63
QM energy of each set in kJ/mol: 270.82 270.81
Peptide omega torsion angles 2.19 degs - monitor only
Weighted rms 0.0085 0.985 (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.