Sun 23 Dec 22:23:02 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 2hoe-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hoe-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-3.6-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/2hoe-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-3.6-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 22:23:11 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/2hoe-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hoe-3.6-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 241 and 0 Target number of residues in the AU: 241 Target solvent content: 0.6686 Checking the provided sequence file Detected sequence length: 380 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 380 Adjusted target solvent content: 0.48 Input MTZ file: 2hoe-3.6-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: 151 Cell parameters: 62.599 62.599 173.950 90.000 90.000 120.000 Input sequence file: 2hoe-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3040 target number of atoms Had to go as low as 0.80 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: 57.983 3.600 Wilson plot Bfac: 90.51 4455 reflections ( 94.11 % complete ) and 0 restraints for refining 3353 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3311 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2883 (Rfree = 0.000) for 3353 atoms. Found 21 (21 requested) and removed 20 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 3423 seeds are put forward Round 1: 140 peptides, 25 chains. Longest chain 24 peptides. Score 0.358 Round 2: 176 peptides, 25 chains. Longest chain 21 peptides. Score 0.501 Round 3: 184 peptides, 23 chains. Longest chain 18 peptides. Score 0.560 Round 4: 190 peptides, 25 chains. Longest chain 29 peptides. Score 0.549 Round 5: 202 peptides, 23 chains. Longest chain 32 peptides. Score 0.616 Taking the results from Round 5 Chains 23, Residues 179, Estimated correctness of the model 20.8 % 4 chains (77 residues) have been docked in sequence ------------------------------------------------------ 4455 reflections ( 94.11 % complete ) and 5488 restraints for refining 2754 atoms. 4520 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2396 (Rfree = 0.000) for 2754 atoms. Found 16 (17 requested) and removed 82 (8 requested) atoms. Cycle 2: After refmac, R = 0.2255 (Rfree = 0.000) for 2624 atoms. Found 10 (17 requested) and removed 15 (8 requested) atoms. Cycle 3: After refmac, R = 0.2191 (Rfree = 0.000) for 2590 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. Cycle 4: After refmac, R = 0.2133 (Rfree = 0.000) for 2555 atoms. Found 3 (16 requested) and removed 17 (8 requested) atoms. Cycle 5: After refmac, R = 0.1814 (Rfree = 0.000) for 2528 atoms. Found 3 (16 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 2641 seeds are put forward Round 1: 179 peptides, 29 chains. Longest chain 33 peptides. Score 0.446 Round 2: 195 peptides, 23 chains. Longest chain 32 peptides. Score 0.595 Round 3: 197 peptides, 28 chains. Longest chain 34 peptides. Score 0.528 Round 4: 218 peptides, 28 chains. Longest chain 33 peptides. Score 0.596 Round 5: 217 peptides, 29 chains. Longest chain 33 peptides. Score 0.579 Taking the results from Round 4 Chains 29, Residues 190, Estimated correctness of the model 13.1 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 4455 reflections ( 94.11 % complete ) and 5399 restraints for refining 2646 atoms. 4503 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2120 (Rfree = 0.000) for 2646 atoms. Found 4 (16 requested) and removed 25 (8 requested) atoms. Cycle 7: After refmac, R = 0.2048 (Rfree = 0.000) for 2600 atoms. Found 16 (16 requested) and removed 18 (8 requested) atoms. Cycle 8: After refmac, R = 0.1908 (Rfree = 0.000) for 2592 atoms. Found 3 (16 requested) and removed 23 (8 requested) atoms. Cycle 9: After refmac, R = 0.2006 (Rfree = 0.000) for 2570 atoms. Found 4 (16 requested) and removed 15 (8 requested) atoms. Cycle 10: After refmac, R = 0.1882 (Rfree = 0.000) for 2556 atoms. Found 7 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.71 Search for helices and strands: 0 residues in 0 chains, 2660 seeds are put forward Round 1: 165 peptides, 28 chains. Longest chain 13 peptides. Score 0.408 Round 2: 199 peptides, 28 chains. Longest chain 18 peptides. Score 0.535 Round 3: 194 peptides, 26 chains. Longest chain 19 peptides. Score 0.548 Round 4: 203 peptides, 27 chains. Longest chain 18 peptides. Score 0.563 Round 5: 199 peptides, 26 chains. Longest chain 24 peptides. Score 0.564 Taking the results from Round 5 Chains 27, Residues 173, Estimated correctness of the model 0.1 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 4455 reflections ( 94.11 % complete ) and 6208 restraints for refining 2755 atoms. 5496 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2017 (Rfree = 0.000) for 2755 atoms. Found 8 (17 requested) and removed 22 (8 requested) atoms. Cycle 12: After refmac, R = 0.1956 (Rfree = 0.000) for 2731 atoms. Found 5 (17 requested) and removed 14 (8 requested) atoms. Cycle 13: After refmac, R = 0.1833 (Rfree = 0.000) for 2715 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. Cycle 14: After refmac, R = 0.1921 (Rfree = 0.000) for 2702 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 15: After refmac, R = 0.2156 (Rfree = 0.000) for 2692 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.59 3.69 Search for helices and strands: 0 residues in 0 chains, 2815 seeds are put forward Round 1: 172 peptides, 31 chains. Longest chain 10 peptides. Score 0.384 Round 2: 192 peptides, 26 chains. Longest chain 18 peptides. Score 0.541 Round 3: 186 peptides, 28 chains. Longest chain 19 peptides. Score 0.489 Round 4: 198 peptides, 27 chains. Longest chain 22 peptides. Score 0.546 Round 5: 199 peptides, 26 chains. Longest chain 19 peptides. Score 0.564 Taking the results from Round 5 Chains 27, Residues 173, Estimated correctness of the model 0.1 % 3 chains (22 residues) have been docked in sequence ------------------------------------------------------ 4455 reflections ( 94.11 % complete ) and 6173 restraints for refining 2756 atoms. 5435 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2044 (Rfree = 0.000) for 2756 atoms. Found 3 (17 requested) and removed 13 (8 requested) atoms. Cycle 17: After refmac, R = 0.1881 (Rfree = 0.000) for 2730 atoms. Found 7 (17 requested) and removed 10 (8 requested) atoms. Cycle 18: After refmac, R = 0.1895 (Rfree = 0.000) for 2724 atoms. Found 4 (17 requested) and removed 11 (8 requested) atoms. Cycle 19: After refmac, R = 0.1919 (Rfree = 0.000) for 2715 atoms. Found 1 (17 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.1806 (Rfree = 0.000) for 2704 atoms. Found 2 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 2801 seeds are put forward Round 1: 150 peptides, 28 chains. Longest chain 13 peptides. Score 0.345 Round 2: 181 peptides, 29 chains. Longest chain 13 peptides. Score 0.454 Round 3: 195 peptides, 29 chains. Longest chain 16 peptides. Score 0.505 Round 4: 191 peptides, 28 chains. Longest chain 17 peptides. Score 0.507 Round 5: 204 peptides, 32 chains. Longest chain 13 peptides. Score 0.491 Taking the results from Round 4 Chains 28, Residues 163, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4455 reflections ( 94.11 % complete ) and 6406 restraints for refining 2756 atoms. 5782 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2037 (Rfree = 0.000) for 2756 atoms. Found 7 (17 requested) and removed 17 (8 requested) atoms. Cycle 22: After refmac, R = 0.2007 (Rfree = 0.000) for 2737 atoms. Found 10 (17 requested) and removed 14 (8 requested) atoms. Cycle 23: After refmac, R = 0.1861 (Rfree = 0.000) for 2726 atoms. Found 1 (17 requested) and removed 12 (8 requested) atoms. Cycle 24: After refmac, R = 0.1541 (Rfree = 0.000) for 2711 atoms. Found 1 (17 requested) and removed 10 (8 requested) atoms. Cycle 25: After refmac, R = 0.1451 (Rfree = 0.000) for 2702 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.65 3.75 Search for helices and strands: 0 residues in 0 chains, 2820 seeds are put forward Round 1: 157 peptides, 29 chains. Longest chain 12 peptides. Score 0.357 Round 2: 170 peptides, 24 chains. Longest chain 15 peptides. Score 0.495 Round 3: 166 peptides, 23 chains. Longest chain 16 peptides. Score 0.497 Round 4: 173 peptides, 27 chains. Longest chain 13 peptides. Score 0.457 Round 5: 164 peptides, 23 chains. Longest chain 16 peptides. Score 0.489 Taking the results from Round 3 Chains 23, Residues 143, Estimated correctness of the model 0.0 % 2 chains (19 residues) have been docked in sequence ------------------------------------------------------ 4455 reflections ( 94.11 % complete ) and 6433 restraints for refining 2756 atoms. 5831 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1783 (Rfree = 0.000) for 2756 atoms. Found 5 (17 requested) and removed 15 (8 requested) atoms. Cycle 27: After refmac, R = 0.1751 (Rfree = 0.000) for 2739 atoms. Found 0 (17 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.1802 (Rfree = 0.000) for 2724 atoms. Found 8 (17 requested) and removed 9 (8 requested) atoms. Cycle 29: After refmac, R = 0.1724 (Rfree = 0.000) for 2720 atoms. Found 10 (17 requested) and removed 14 (8 requested) atoms. Cycle 30: After refmac, R = 0.1629 (Rfree = 0.000) for 2713 atoms. Found 2 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 2809 seeds are put forward Round 1: 139 peptides, 27 chains. Longest chain 11 peptides. Score 0.316 Round 2: 161 peptides, 25 chains. Longest chain 14 peptides. Score 0.444 Round 3: 154 peptides, 23 chains. Longest chain 17 peptides. Score 0.451 Round 4: 152 peptides, 22 chains. Longest chain 16 peptides. Score 0.461 Round 5: 156 peptides, 22 chains. Longest chain 15 peptides. Score 0.476 Taking the results from Round 5 Chains 22, Residues 134, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4455 reflections ( 94.11 % complete ) and 6485 restraints for refining 2756 atoms. 5928 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1770 (Rfree = 0.000) for 2756 atoms. Found 8 (17 requested) and removed 11 (8 requested) atoms. Cycle 32: After refmac, R = 0.1646 (Rfree = 0.000) for 2748 atoms. Found 2 (17 requested) and removed 12 (8 requested) atoms. Cycle 33: After refmac, R = 0.1370 (Rfree = 0.000) for 2736 atoms. Found 1 (17 requested) and removed 9 (8 requested) atoms. Cycle 34: After refmac, R = 0.1297 (Rfree = 0.000) for 2728 atoms. Found 1 (17 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.1271 (Rfree = 0.000) for 2719 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.76 Search for helices and strands: 0 residues in 0 chains, 2843 seeds are put forward Round 1: 129 peptides, 26 chains. Longest chain 9 peptides. Score 0.290 Round 2: 157 peptides, 26 chains. Longest chain 13 peptides. Score 0.411 Round 3: 153 peptides, 24 chains. Longest chain 18 peptides. Score 0.430 Round 4: 156 peptides, 26 chains. Longest chain 14 peptides. Score 0.407 Round 5: 163 peptides, 23 chains. Longest chain 17 peptides. Score 0.486 Taking the results from Round 5 Chains 23, Residues 140, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4455 reflections ( 94.11 % complete ) and 6568 restraints for refining 2756 atoms. 6031 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1896 (Rfree = 0.000) for 2756 atoms. Found 7 (17 requested) and removed 8 (8 requested) atoms. Cycle 37: After refmac, R = 0.1728 (Rfree = 0.000) for 2748 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. Cycle 38: After refmac, R = 0.1660 (Rfree = 0.000) for 2744 atoms. Found 1 (17 requested) and removed 9 (8 requested) atoms. Cycle 39: After refmac, R = 0.1651 (Rfree = 0.000) for 2732 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. Cycle 40: After refmac, R = 0.1756 (Rfree = 0.000) for 2723 atoms. Found 10 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.64 3.74 Search for helices and strands: 0 residues in 0 chains, 2816 seeds are put forward Round 1: 140 peptides, 30 chains. Longest chain 8 peptides. Score 0.263 Round 2: 146 peptides, 23 chains. Longest chain 11 peptides. Score 0.419 Round 3: 152 peptides, 23 chains. Longest chain 11 peptides. Score 0.444 Round 4: 153 peptides, 24 chains. Longest chain 12 peptides. Score 0.430 Round 5: 150 peptides, 22 chains. Longest chain 18 peptides. Score 0.453 Taking the results from Round 5 Chains 26, Residues 128, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 4455 reflections ( 94.11 % complete ) and 6376 restraints for refining 2756 atoms. 5810 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1861 (Rfree = 0.000) for 2756 atoms. Found 8 (17 requested) and removed 12 (8 requested) atoms. Cycle 42: After refmac, R = 0.1680 (Rfree = 0.000) for 2747 atoms. Found 1 (17 requested) and removed 8 (8 requested) atoms. Cycle 43: After refmac, R = 0.1573 (Rfree = 0.000) for 2738 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 44: After refmac, R = 0.1540 (Rfree = 0.000) for 2728 atoms. Found 0 (17 requested) and removed 9 (8 requested) atoms. Cycle 45: After refmac, R = 0.1526 (Rfree = 0.000) for 2718 atoms. Found 3 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.77 Search for helices and strands: 0 residues in 0 chains, 2797 seeds are put forward Round 1: 123 peptides, 26 chains. Longest chain 8 peptides. Score 0.261 Round 2: 136 peptides, 24 chains. Longest chain 12 peptides. Score 0.359 Round 3: 129 peptides, 22 chains. Longest chain 16 peptides. Score 0.367 Round 4: 133 peptides, 24 chains. Longest chain 9 peptides. Score 0.346 Round 5: 148 peptides, 23 chains. Longest chain 17 peptides. Score 0.428 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 125, Estimated correctness of the model 0.0 % 3 chains (23 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 2hoe-3_warpNtrace.pdb as input Building loops using Loopy2018 25 chains (125 residues) following loop building 3 chains (23 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4455 reflections ( 94.11 % complete ) and 6364 restraints for refining 2756 atoms. 5804 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1932 (Rfree = 0.000) for 2756 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.1798 (Rfree = 0.000) for 2745 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.1758 (Rfree = 0.000) for 2736 atoms. Found 0 (17 requested) and removed 2 (8 requested) atoms. Cycle 49: After refmac, R = 0.1731 (Rfree = 0.000) for 2734 atoms. TimeTaking 51.03