################################################################# ################################################################# ########## LOw REsolution STructure Refinement pipeline ######### ######################### (LORESTR) ############################# ############### Version D6 ############## Dec 2022 ############## ################################################################# ## Copyright (C) 2015-2022 Oleg Kovalevskiy, Robert Nicholls ## ## and Garib Murshudov ## ## ## ## LORESTR is distributed in the hope that it will be useful, ## ## but WITHOUT ANY WARRANTY; without even the implied warranty ## ## of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ## ## See the GNU Lesser General Public License (v3) for details. ## ## The authors accept no liability whatsoever for any damage ## ## caused by the use or misuse of this software. ## ## ## ## E-mail: ccp4@ccp4.ac.uk ## ## ## ################################################################# Working in: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/ccp4/lorestr_Output/ MolProbity detected (molprobity.molprobity); geometrical quality will be assesed Program received following parameters: Target structure: ../original/1fb5/1fb5.pdb Data for target structure: ../original/1fb5/1fb5.mtz Supplied homologous structures: None Number of CPUs to use: 1 Analysing protein chains: A ...done. 1 protein chain(s) with unique sequence found. Auto selection of homologues: Running BLAST search... Chain A: Found 5 PDB structures and 10 AF models. 1fb5 : Aligned 100%, Sequence identity 100% - accepted for restraints generation 1c9y : Aligned 100%, Sequence identity 98% - accepted for restraints generation 1ep9 : Aligned 100%, Sequence identity 98% - accepted for restraints generation 1fvo : Aligned 100%, Sequence identity 98% - accepted for restraints generation 1oth : Aligned 100%, Sequence identity 98% - accepted for restraints generation AF-P00480-F1 : Aligned 99%, Sequence identity 97% - accepted for restraints generation AF-P84010-F1 : Aligned 99%, Sequence identity 94% - accepted for restraints generation AF-Q9N1U7-F1 : Aligned 99%, Sequence identity 93% - accepted for restraints generation AF-P11725-F1 : Aligned 99%, Sequence identity 93% - accepted for restraints generation AF-O19072-F1 : Aligned 99%, Sequence identity 92% - accepted for restraints generation Analysing input files: Analysing data for twinning... no twinning detected. Checking best scaling option... standard scaling performed better; will use standard scaling for REFMAC. Figuring out solvent modelling parameters... done. Using following solvent parameters: VDWProb 1.00, IONProb 0.90, RSHRink 0.90 Figuring out starting refinement statistics... done. Starting from Rfact: 0.204 and Rfree: 0.245 Ramachandran outliers: 7.86% Ramachandran favoured: 71.38% Clashscore percentile: 7.10 Molprobity percentile: 5.50 Analysing external homologues... done. Initialising refinement protocol(s)... Using default set of protocols for refinement: 1 - Jelly body only 2 - External restraints from 1 closest homologue(s) (H-bonds for chains without suitable homologue), then jelly body: 1fb5.pdb, chain A: restraints from 1fvo.pdb, chain A. Sequence identity: 0.98, local RMSD: 0.32, global RMSD: 1.25 3 - External restraints from 2 closest homologue(s) (H-bonds for chains without suitable homologue), then jelly body: 1fb5.pdb, chain A: restraints from 1fvo.pdb, chain A. Sequence identity: 0.98, local RMSD: 0.32, global RMSD: 1.25 1fb5.pdb, chain A: restraints from AF-O19072-F1.pdb, chain A. Sequence identity: 0.93, local RMSD: 0.32, global RMSD: 1.26 4 - External restraints from 3 closest homologue(s) (H-bonds for chains without suitable homologue), then jelly body: 1fb5.pdb, chain A: restraints from 1fvo.pdb, chain A. Sequence identity: 0.98, local RMSD: 0.32, global RMSD: 1.25 1fb5.pdb, chain A: restraints from AF-O19072-F1.pdb, chain A. Sequence identity: 0.93, local RMSD: 0.32, global RMSD: 1.26 1fb5.pdb, chain A: restraints from AF-Q9N1U7-F1.pdb, chain A. Sequence identity: 0.94, local RMSD: 0.32, global RMSD: 1.27 5 - External restraints from all the homologues (-restrain_all), then jelly body: AF-P11725-F1.pdb 1oth.pdb 1c9y.pdb 1ep9.pdb AF-Q9N1U7-F1.pdb AF-O19072-F1.pdb AF-P84010-F1.pdb AF-P00480-F1.pdb 1fvo.pdb 6 - External restraints from all the homologues (-restrain_best), then jelly body: AF-P11725-F1.pdb 1oth.pdb 1c9y.pdb 1ep9.pdb AF-Q9N1U7-F1.pdb AF-O19072-F1.pdb AF-P84010-F1.pdb AF-P00480-F1.pdb 1fvo.pdb 7 - External restraints from 1 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body: 1fb5.pdb, chain A: restraints from 1oth.pdb, chain A. Sequence identity: 0.98, local RMSD: 0.32, global RMSD: 1.36 8 - External restraints from 2 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body: 1fb5.pdb, chain A: restraints from 1oth.pdb, chain A. Sequence identity: 0.98, local RMSD: 0.32, global RMSD: 1.36 1fb5.pdb, chain A: restraints from 1ep9.pdb, chain A. Sequence identity: 0.98, local RMSD: 0.32, global RMSD: 1.34 9 - External restraints from 3 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body: 1fb5.pdb, chain A: restraints from 1oth.pdb, chain A. Sequence identity: 0.98, local RMSD: 0.32, global RMSD: 1.36 1fb5.pdb, chain A: restraints from 1ep9.pdb, chain A. Sequence identity: 0.98, local RMSD: 0.32, global RMSD: 1.34 1fb5.pdb, chain A: restraints from 1c9y.pdb, chain A. Sequence identity: 0.98, local RMSD: 0.32, global RMSD: 1.34 10 - Hydrogen bonds restraints for all chains: 1fb5.pdb, chain A: H-bonds restraints Refinement protocol(s) successfully initialised. Running refinement protocol(s)... Starting protocol 1 out of 10 (Jelly body only) Protocol 1 out of 10 (Jelly body only) finished. Rfact: 0.181, Rfree: 0.217 Ramachandran outliers: 7.23% Ramachandran favoured: 71.38% Clashscore percentile: 6.80 Molprobity percentile: 4.80 Starting protocol 2 out of 10 (External restraints from 1 closest homologue(s) (H-bonds for chains without suitable homologue), then jelly body) Protocol 2 out of 10 (External restraints from 1 closest homologue(s) (H-bonds for chains without suitable homologue), then jelly body) finished. Rfact: 0.175, Rfree: 0.207 Ramachandran outliers: 5.35% Ramachandran favoured: 88.36% Clashscore percentile: 11.80 Molprobity percentile: 9.70 Starting protocol 3 out of 10 (External restraints from 2 closest homologue(s) (H-bonds for chains without suitable homologue), then jelly body) Protocol 3 out of 10 (External restraints from 2 closest homologue(s) (H-bonds for chains without suitable homologue), then jelly body) finished. Rfact: 0.172, Rfree: 0.207 Ramachandran outliers: 4.09% Ramachandran favoured: 89.94% Clashscore percentile: 14.80 Molprobity percentile: 12.50 Starting protocol 4 out of 10 (External restraints from 3 closest homologue(s) (H-bonds for chains without suitable homologue), then jelly body) Protocol 4 out of 10 (External restraints from 3 closest homologue(s) (H-bonds for chains without suitable homologue), then jelly body) finished. Rfact: 0.173, Rfree: 0.211 Ramachandran outliers: 3.77% Ramachandran favoured: 88.68% Clashscore percentile: 13.40 Molprobity percentile: 12.30 Starting protocol 5 out of 10 (External restraints from all the homologues (-restrain_all), then jelly body) Protocol 5 out of 10 (External restraints from all the homologues (-restrain_all), then jelly body) finished. Rfact: 0.172, Rfree: 0.205 Ramachandran outliers: 5.03% Ramachandran favoured: 87.11% Clashscore percentile: 10.90 Molprobity percentile: 10.10 Starting protocol 6 out of 10 (External restraints from all the homologues (-restrain_best), then jelly body) Protocol 6 out of 10 (External restraints from all the homologues (-restrain_best), then jelly body) finished. Rfact: 0.172, Rfree: 0.210 Ramachandran outliers: 4.72% Ramachandran favoured: 88.05% Clashscore percentile: 12.20 Molprobity percentile: 10.50 Starting protocol 7 out of 10 (External restraints from 1 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body) Protocol 7 out of 10 (External restraints from 1 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body) finished. Rfact: 0.175, Rfree: 0.212 Ramachandran outliers: 5.03% Ramachandran favoured: 90.88% Clashscore percentile: 14.30 Molprobity percentile: 13.40 Starting protocol 8 out of 10 (External restraints from 2 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body) Protocol 8 out of 10 (External restraints from 2 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body) finished. Rfact: 0.172, Rfree: 0.205 Ramachandran outliers: 4.72% Ramachandran favoured: 89.31% Clashscore percentile: 14.30 Molprobity percentile: 11.70 Starting protocol 9 out of 10 (External restraints from 3 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body) Protocol 9 out of 10 (External restraints from 3 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body) finished. Rfact: 0.172, Rfree: 0.206 Ramachandran outliers: 4.40% Ramachandran favoured: 89.62% Clashscore percentile: 15.10 Molprobity percentile: 12.90 Starting protocol 10 out of 10 (Hydrogen bonds restraints for all chains) Protocol 10 out of 10 (Hydrogen bonds restraints for all chains) finished. Rfact: 0.167, Rfree: 0.212 Ramachandran outliers: 9.75% Ramachandran favoured: 75.79% Clashscore percentile: 6.40 Molprobity percentile: 2.90 All refinement protocols have finished. Statistics for LORESTR run and the best protocol: Worst Rfree value: 0.217, Best Rfree value: 0.205 Worst Molprobity percentile: 2.90, Best Molprobity percentile: 13.40 Protocol 1 : Rfree 0.217, Molprobity percentile 4.80, Qscore 22.68 Protocol 2 : Rfree 0.207, Molprobity percentile 9.70, Qscore 21.12 Protocol 3 : Rfree 0.207, Molprobity percentile 12.50, Qscore 20.80 Protocol 4 : Rfree 0.211, Molprobity percentile 12.30, Qscore 21.23 Protocol 5 : Rfree 0.205, Molprobity percentile 10.10, Qscore 20.88 Protocol 6 : Rfree 0.210, Molprobity percentile 10.50, Qscore 21.33 Protocol 7 : Rfree 0.212, Molprobity percentile 13.40, Qscore 21.20 Protocol 8 : Rfree 0.205, Molprobity percentile 11.70, Qscore 20.69 Protocol 9 : Rfree 0.206, Molprobity percentile 12.90, Qscore 20.66 Protocol 10 : Rfree 0.212, Molprobity percentile 2.90, Qscore 22.40 Best performing protocol (basing on Qscore): 9 - External restraints from 3 most distant homologue(s) (H-bonds for chains without suitable homologue), then jelly body Rfact (before/after): 0.204 / 0.172 Rfree (before/after): 0.245 / 0.206 Ramachandran outliers (before/after): 7.86% / 4.40% Ramachandran favoured (before/after): 71.38% / 89.62% Clashscore percentile (before/after): 7.10 / 15.10 Molprobity percentile (before/after): 5.50 / 12.90 Final PDB file after refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/ccp4/lorestr_Output/1fb5_best.pdb Final MTZ file after refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/ccp4/lorestr_Output/1fb5_best.mtz