Sun 23 Dec 22:22:40 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hsb-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hsb-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hsb-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-4.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-4.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:22:49 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hsb-4.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 94 and 0 Target number of residues in the AU: 94 Target solvent content: 0.6559 Checking the provided sequence file Detected sequence length: 126 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 126 Adjusted target solvent content: 0.54 Input MTZ file: 2hsb-4.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 96 Cell parameters: 60.666 60.666 80.341 90.000 90.000 90.000 Input sequence file: 2hsb-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1008 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 Loops will be built when appropriate and at the last cycle Resolution range: 48.414 4.000 Wilson plot Bfac: 80.25 1443 reflections ( 99.65 % complete ) and 0 restraints for refining 1112 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3789 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3788 (Rfree = 0.000) for 1112 atoms. Found 4 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 5.23 4.96 Search for helices and strands: 0 residues in 0 chains, 1148 seeds are put forward Round 1: 34 peptides, 7 chains. Longest chain 6 peptides. Score 0.254 Round 2: 50 peptides, 9 chains. Longest chain 8 peptides. Score 0.347 Round 3: 50 peptides, 7 chains. Longest chain 11 peptides. Score 0.446 Round 4: 47 peptides, 7 chains. Longest chain 12 peptides. Score 0.413 Round 5: 51 peptides, 8 chains. Longest chain 12 peptides. Score 0.408 Taking the results from Round 3 Chains 7, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1443 reflections ( 99.65 % complete ) and 1933 restraints for refining 827 atoms. 1768 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3411 (Rfree = 0.000) for 827 atoms. Found 2 (3 requested) and removed 10 (1 requested) atoms. Cycle 2: After refmac, R = 0.3477 (Rfree = 0.000) for 804 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 3: After refmac, R = 0.3522 (Rfree = 0.000) for 789 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 4: After refmac, R = 0.3421 (Rfree = 0.000) for 775 atoms. Found 3 (3 requested) and removed 8 (1 requested) atoms. Cycle 5: After refmac, R = 0.3361 (Rfree = 0.000) for 754 atoms. Found 2 (3 requested) and removed 5 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 797 seeds are put forward Round 1: 52 peptides, 11 chains. Longest chain 7 peptides. Score 0.269 Round 2: 58 peptides, 9 chains. Longest chain 13 peptides. Score 0.436 Round 3: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.399 Round 4: 53 peptides, 9 chains. Longest chain 8 peptides. Score 0.381 Round 5: 47 peptides, 8 chains. Longest chain 8 peptides. Score 0.363 Taking the results from Round 2 Chains 9, Residues 49, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1443 reflections ( 99.65 % complete ) and 1583 restraints for refining 738 atoms. 1396 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2833 (Rfree = 0.000) for 738 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 7: After refmac, R = 0.2731 (Rfree = 0.000) for 732 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 8: After refmac, R = 0.2554 (Rfree = 0.000) for 730 atoms. Found 1 (3 requested) and removed 5 (1 requested) atoms. Cycle 9: After refmac, R = 0.2504 (Rfree = 0.000) for 723 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 10: After refmac, R = 0.2399 (Rfree = 0.000) for 722 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.58 3.39 Search for helices and strands: 0 residues in 0 chains, 761 seeds are put forward Round 1: 56 peptides, 11 chains. Longest chain 7 peptides. Score 0.317 Round 2: 60 peptides, 10 chains. Longest chain 12 peptides. Score 0.410 Round 3: 59 peptides, 9 chains. Longest chain 10 peptides. Score 0.446 Round 4: 60 peptides, 9 chains. Longest chain 15 peptides. Score 0.456 Round 5: 64 peptides, 9 chains. Longest chain 13 peptides. Score 0.496 Taking the results from Round 5 Chains 9, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1443 reflections ( 99.65 % complete ) and 1700 restraints for refining 798 atoms. 1489 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2704 (Rfree = 0.000) for 798 atoms. Found 3 (3 requested) and removed 18 (1 requested) atoms. Cycle 12: After refmac, R = 0.3010 (Rfree = 0.000) for 780 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 13: After refmac, R = 0.2686 (Rfree = 0.000) for 771 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 14: After refmac, R = 0.2540 (Rfree = 0.000) for 764 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 15: After refmac, R = 0.2189 (Rfree = 0.000) for 760 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.64 3.45 Search for helices and strands: 0 residues in 0 chains, 800 seeds are put forward Round 1: 48 peptides, 10 chains. Longest chain 7 peptides. Score 0.271 Round 2: 48 peptides, 8 chains. Longest chain 11 peptides. Score 0.374 Round 3: 57 peptides, 9 chains. Longest chain 9 peptides. Score 0.425 Round 4: 58 peptides, 10 chains. Longest chain 8 peptides. Score 0.388 Round 5: 47 peptides, 6 chains. Longest chain 11 peptides. Score 0.463 Taking the results from Round 5 Chains 6, Residues 41, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1443 reflections ( 99.65 % complete ) and 1795 restraints for refining 800 atoms. 1637 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3141 (Rfree = 0.000) for 800 atoms. Found 3 (3 requested) and removed 11 (1 requested) atoms. Cycle 17: After refmac, R = 0.2698 (Rfree = 0.000) for 781 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 18: After refmac, R = 0.3115 (Rfree = 0.000) for 766 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 19: After refmac, R = 0.2676 (Rfree = 0.000) for 757 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 20: After refmac, R = 0.3235 (Rfree = 0.000) for 749 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.69 3.50 Search for helices and strands: 0 residues in 0 chains, 782 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 6 peptides. Score 0.218 Round 2: 54 peptides, 10 chains. Longest chain 9 peptides. Score 0.343 Round 3: 61 peptides, 10 chains. Longest chain 12 peptides. Score 0.421 Round 4: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.374 Round 5: 63 peptides, 9 chains. Longest chain 12 peptides. Score 0.486 Taking the results from Round 5 Chains 9, Residues 54, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 1443 reflections ( 99.65 % complete ) and 1527 restraints for refining 776 atoms. 1277 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2904 (Rfree = 0.000) for 776 atoms. Found 3 (3 requested) and removed 11 (1 requested) atoms. Cycle 22: After refmac, R = 0.2480 (Rfree = 0.000) for 759 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 23: After refmac, R = 0.2277 (Rfree = 0.000) for 753 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 24: After refmac, R = 0.2279 (Rfree = 0.000) for 749 atoms. Found 1 (3 requested) and removed 4 (1 requested) atoms. Cycle 25: After refmac, R = 0.2414 (Rfree = 0.000) for 743 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.78 3.58 Search for helices and strands: 0 residues in 0 chains, 788 seeds are put forward Round 1: 46 peptides, 9 chains. Longest chain 8 peptides. Score 0.299 Round 2: 55 peptides, 8 chains. Longest chain 13 peptides. Score 0.451 Round 3: 52 peptides, 9 chains. Longest chain 10 peptides. Score 0.370 Round 4: 54 peptides, 10 chains. Longest chain 10 peptides. Score 0.343 Round 5: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.377 Taking the results from Round 2 Chains 8, Residues 47, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1443 reflections ( 99.65 % complete ) and 1640 restraints for refining 758 atoms. 1460 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3181 (Rfree = 0.000) for 758 atoms. Found 3 (3 requested) and removed 10 (1 requested) atoms. Cycle 27: After refmac, R = 0.2931 (Rfree = 0.000) for 747 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 28: After refmac, R = 0.2785 (Rfree = 0.000) for 744 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 29: After refmac, R = 0.2965 (Rfree = 0.000) for 740 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 30: After refmac, R = 0.2778 (Rfree = 0.000) for 739 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 3.57 Search for helices and strands: 0 residues in 0 chains, 780 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 8 peptides. Score 0.274 Round 2: 40 peptides, 7 chains. Longest chain 8 peptides. Score 0.331 Round 3: 41 peptides, 7 chains. Longest chain 10 peptides. Score 0.344 Round 4: 44 peptides, 8 chains. Longest chain 8 peptides. Score 0.327 Round 5: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.327 Taking the results from Round 3 Chains 7, Residues 34, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1443 reflections ( 99.65 % complete ) and 1590 restraints for refining 734 atoms. 1461 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2671 (Rfree = 0.000) for 734 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 32: After refmac, R = 0.2806 (Rfree = 0.000) for 728 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 33: After refmac, R = 0.2481 (Rfree = 0.000) for 725 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. Cycle 34: After refmac, R = 0.2424 (Rfree = 0.000) for 723 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. Cycle 35: After refmac, R = 0.2236 (Rfree = 0.000) for 720 atoms. Found 0 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.76 3.56 Search for helices and strands: 0 residues in 0 chains, 751 seeds are put forward Round 1: 44 peptides, 8 chains. Longest chain 9 peptides. Score 0.327 Round 2: 60 peptides, 11 chains. Longest chain 14 peptides. Score 0.363 Round 3: 47 peptides, 8 chains. Longest chain 10 peptides. Score 0.363 Round 4: 45 peptides, 7 chains. Longest chain 10 peptides. Score 0.391 Round 5: 43 peptides, 6 chains. Longest chain 12 peptides. Score 0.419 Taking the results from Round 5 Chains 6, Residues 37, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1443 reflections ( 99.65 % complete ) and 1818 restraints for refining 809 atoms. 1676 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2608 (Rfree = 0.000) for 809 atoms. Found 3 (3 requested) and removed 10 (1 requested) atoms. Cycle 37: After refmac, R = 0.2271 (Rfree = 0.000) for 800 atoms. Found 1 (3 requested) and removed 5 (1 requested) atoms. Cycle 38: After refmac, R = 0.2066 (Rfree = 0.000) for 795 atoms. Found 1 (3 requested) and removed 3 (1 requested) atoms. Cycle 39: After refmac, R = 0.1884 (Rfree = 0.000) for 792 atoms. Found 0 (3 requested) and removed 9 (1 requested) atoms. Cycle 40: After refmac, R = 0.1893 (Rfree = 0.000) for 783 atoms. Found 0 (3 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.71 3.52 Search for helices and strands: 0 residues in 0 chains, 812 seeds are put forward Round 1: 40 peptides, 8 chains. Longest chain 10 peptides. Score 0.277 Round 2: 42 peptides, 9 chains. Longest chain 6 peptides. Score 0.248 Round 3: 47 peptides, 8 chains. Longest chain 8 peptides. Score 0.363 Round 4: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.267 Round 5: 40 peptides, 7 chains. Longest chain 9 peptides. Score 0.331 Taking the results from Round 3 Chains 8, Residues 39, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1443 reflections ( 99.65 % complete ) and 1895 restraints for refining 832 atoms. 1747 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2157 (Rfree = 0.000) for 832 atoms. Found 3 (3 requested) and removed 24 (1 requested) atoms. Cycle 42: After refmac, R = 0.1971 (Rfree = 0.000) for 806 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 43: After refmac, R = 0.1891 (Rfree = 0.000) for 802 atoms. Found 2 (3 requested) and removed 8 (1 requested) atoms. Cycle 44: After refmac, R = 0.1853 (Rfree = 0.000) for 795 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 45: After refmac, R = 0.1810 (Rfree = 0.000) for 793 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 829 seeds are put forward Round 1: 29 peptides, 7 chains. Longest chain 5 peptides. Score 0.182 Round 2: 39 peptides, 9 chains. Longest chain 5 peptides. Score 0.208 Round 3: 39 peptides, 9 chains. Longest chain 5 peptides. Score 0.208 Round 4: 40 peptides, 9 chains. Longest chain 5 peptides. Score 0.222 Round 5: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.315 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2hsb-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1443 reflections ( 99.65 % complete ) and 1815 restraints for refining 814 atoms. 1683 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2503 (Rfree = 0.000) for 814 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.2327 (Rfree = 0.000) for 807 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.3320 (Rfree = 0.000) for 805 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.2298 (Rfree = 0.000) for 801 atoms. TimeTaking 20.95