null Tue 25 Dec 19:27:55 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 1zyb-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-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/1zyb-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-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 ============================================================ Tue 25 Dec 19:28:05 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/1zyb-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-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 301 and 0 Target number of residues in the AU: 301 Target solvent content: 0.6494 Checking the provided sequence file Detected sequence length: 232 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 232 Adjusted target solvent content: 0.73 Input MTZ file: 1zyb-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: 179 Cell parameters: 115.980 115.980 119.640 90.000 90.000 120.000 Input sequence file: 1zyb-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 1856 target number of atoms Had to go as low as 1.30 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: 100.441 3.600 Wilson plot Bfac: 77.36 5867 reflections ( 99.34 % complete ) and 0 restraints for refining 2086 atoms. Observations/parameters ratio is 0.70 ------------------------------------------------------ Starting model: R = 0.3830 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3543 (Rfree = 0.000) for 2086 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 2126 seeds are put forward Round 1: 156 peptides, 19 chains. Longest chain 25 peptides. Score 0.488 Round 2: 162 peptides, 19 chains. Longest chain 26 peptides. Score 0.507 Round 3: 169 peptides, 17 chains. Longest chain 25 peptides. Score 0.557 Round 4: 184 peptides, 15 chains. Longest chain 40 peptides. Score 0.625 Round 5: 172 peptides, 16 chains. Longest chain 35 peptides. Score 0.579 Taking the results from Round 4 Chains 15, Residues 169, Estimated correctness of the model 24.2 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5867 reflections ( 99.34 % complete ) and 3443 restraints for refining 1682 atoms. 2782 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2805 (Rfree = 0.000) for 1682 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 2: After refmac, R = 0.2689 (Rfree = 0.000) for 1655 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 3: After refmac, R = 0.2564 (Rfree = 0.000) for 1649 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 4: After refmac, R = 0.2441 (Rfree = 0.000) for 1639 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. Cycle 5: After refmac, R = 0.2408 (Rfree = 0.000) for 1635 atoms. Found 9 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.45 2.48 Search for helices and strands: 0 residues in 0 chains, 1735 seeds are put forward Round 1: 184 peptides, 16 chains. Longest chain 32 peptides. Score 0.612 Round 2: 183 peptides, 13 chains. Longest chain 50 peptides. Score 0.647 Round 3: 178 peptides, 15 chains. Longest chain 26 peptides. Score 0.609 Round 4: 184 peptides, 14 chains. Longest chain 31 peptides. Score 0.637 Round 5: 191 peptides, 15 chains. Longest chain 25 peptides. Score 0.642 Taking the results from Round 2 Chains 13, Residues 170, Estimated correctness of the model 32.1 % 1 chains (49 residues) have been docked in sequence ------------------------------------------------------ 5867 reflections ( 99.34 % complete ) and 2896 restraints for refining 1682 atoms. 2006 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2945 (Rfree = 0.000) for 1682 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 7: After refmac, R = 0.2822 (Rfree = 0.000) for 1668 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 8: After refmac, R = 0.2675 (Rfree = 0.000) for 1666 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 9: After refmac, R = 0.2663 (Rfree = 0.000) for 1668 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 10: After refmac, R = 0.2549 (Rfree = 0.000) for 1665 atoms. Found 6 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 2.51 Search for helices and strands: 0 residues in 0 chains, 1725 seeds are put forward Round 1: 171 peptides, 19 chains. Longest chain 18 peptides. Score 0.535 Round 2: 172 peptides, 14 chains. Longest chain 25 peptides. Score 0.606 Round 3: 176 peptides, 17 chains. Longest chain 24 peptides. Score 0.577 Round 4: 173 peptides, 18 chains. Longest chain 25 peptides. Score 0.555 Round 5: 176 peptides, 17 chains. Longest chain 32 peptides. Score 0.577 Taking the results from Round 2 Chains 14, Residues 158, Estimated correctness of the model 17.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5867 reflections ( 99.34 % complete ) and 3551 restraints for refining 1683 atoms. 2933 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2647 (Rfree = 0.000) for 1683 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 12: After refmac, R = 0.2395 (Rfree = 0.000) for 1683 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 13: After refmac, R = 0.2283 (Rfree = 0.000) for 1676 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. Cycle 14: After refmac, R = 0.2321 (Rfree = 0.000) for 1672 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 15: After refmac, R = 0.2138 (Rfree = 0.000) for 1674 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.46 2.48 Search for helices and strands: 0 residues in 0 chains, 1738 seeds are put forward Round 1: 171 peptides, 21 chains. Longest chain 19 peptides. Score 0.506 Round 2: 176 peptides, 20 chains. Longest chain 19 peptides. Score 0.536 Round 3: 182 peptides, 18 chains. Longest chain 23 peptides. Score 0.580 Round 4: 195 peptides, 15 chains. Longest chain 47 peptides. Score 0.652 Round 5: 177 peptides, 16 chains. Longest chain 21 peptides. Score 0.593 Taking the results from Round 4 Chains 18, Residues 180, Estimated correctness of the model 33.9 % 2 chains (50 residues) have been docked in sequence ------------------------------------------------------ 5867 reflections ( 99.34 % complete ) and 2813 restraints for refining 1683 atoms. 1913 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2795 (Rfree = 0.000) for 1683 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 17: After refmac, R = 0.2614 (Rfree = 0.000) for 1670 atoms. Found 10 (10 requested) and removed 9 (5 requested) atoms. Cycle 18: After refmac, R = 0.2550 (Rfree = 0.000) for 1663 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 19: After refmac, R = 0.2475 (Rfree = 0.000) for 1660 atoms. Found 4 (10 requested) and removed 5 (5 requested) atoms. Cycle 20: After refmac, R = 0.2437 (Rfree = 0.000) for 1656 atoms. Found 1 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.49 2.51 Search for helices and strands: 0 residues in 0 chains, 1707 seeds are put forward Round 1: 169 peptides, 19 chains. Longest chain 21 peptides. Score 0.529 Round 2: 178 peptides, 18 chains. Longest chain 22 peptides. Score 0.569 Round 3: 172 peptides, 16 chains. Longest chain 29 peptides. Score 0.579 Round 4: 178 peptides, 18 chains. Longest chain 23 peptides. Score 0.569 Round 5: 172 peptides, 20 chains. Longest chain 25 peptides. Score 0.524 Taking the results from Round 3 Chains 16, Residues 156, Estimated correctness of the model 6.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5867 reflections ( 99.34 % complete ) and 3476 restraints for refining 1683 atoms. 2868 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2765 (Rfree = 0.000) for 1683 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 22: After refmac, R = 0.2474 (Rfree = 0.000) for 1678 atoms. Found 10 (10 requested) and removed 6 (5 requested) atoms. Cycle 23: After refmac, R = 0.2365 (Rfree = 0.000) for 1676 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. Cycle 24: After refmac, R = 0.2325 (Rfree = 0.000) for 1672 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 25: After refmac, R = 0.2332 (Rfree = 0.000) for 1675 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.53 2.53 Search for helices and strands: 0 residues in 0 chains, 1762 seeds are put forward Round 1: 159 peptides, 19 chains. Longest chain 19 peptides. Score 0.498 Round 2: 178 peptides, 17 chains. Longest chain 29 peptides. Score 0.583 Round 3: 177 peptides, 20 chains. Longest chain 21 peptides. Score 0.539 Round 4: 187 peptides, 18 chains. Longest chain 22 peptides. Score 0.594 Round 5: 177 peptides, 17 chains. Longest chain 41 peptides. Score 0.580 Taking the results from Round 4 Chains 18, Residues 169, Estimated correctness of the model 12.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5867 reflections ( 99.34 % complete ) and 3402 restraints for refining 1683 atoms. 2744 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2744 (Rfree = 0.000) for 1683 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 27: After refmac, R = 0.2425 (Rfree = 0.000) for 1676 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 28: After refmac, R = 0.2325 (Rfree = 0.000) for 1677 atoms. Found 3 (10 requested) and removed 5 (5 requested) atoms. Cycle 29: After refmac, R = 0.2295 (Rfree = 0.000) for 1672 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 30: After refmac, R = 0.2195 (Rfree = 0.000) for 1674 atoms. Found 5 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 2.51 Search for helices and strands: 0 residues in 0 chains, 1762 seeds are put forward Round 1: 180 peptides, 19 chains. Longest chain 21 peptides. Score 0.561 Round 2: 183 peptides, 15 chains. Longest chain 29 peptides. Score 0.622 Round 3: 184 peptides, 17 chains. Longest chain 28 peptides. Score 0.599 Round 4: 189 peptides, 18 chains. Longest chain 26 peptides. Score 0.599 Round 5: 184 peptides, 17 chains. Longest chain 27 peptides. Score 0.599 Taking the results from Round 2 Chains 15, Residues 168, Estimated correctness of the model 23.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 5867 reflections ( 99.34 % complete ) and 3445 restraints for refining 1682 atoms. 2788 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2530 (Rfree = 0.000) for 1682 atoms. Found 10 (10 requested) and removed 7 (5 requested) atoms. Cycle 32: After refmac, R = 0.2331 (Rfree = 0.000) for 1673 atoms. Found 7 (10 requested) and removed 6 (5 requested) atoms. Cycle 33: After refmac, R = 0.2273 (Rfree = 0.000) for 1667 atoms. Found 9 (10 requested) and removed 6 (5 requested) atoms. Cycle 34: After refmac, R = 0.2197 (Rfree = 0.000) for 1667 atoms. Found 6 (10 requested) and removed 5 (5 requested) atoms. Cycle 35: After refmac, R = 0.2172 (Rfree = 0.000) for 1668 atoms. Found 7 (10 requested) and removed 5 (5 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.51 2.52 Search for helices and strands: 0 residues in 0 chains, 1736 seeds are put forward Round 1: 165 peptides, 21 chains. Longest chain 19 peptides. Score 0.487 Round 2: 179 peptides, 17 chains. Longest chain 20 peptides. Score 0.585 Round 3: 187 peptides, 18 chains. Longest chain 25 peptides. Score 0.594 Round 4: 191 peptides, 17 chains. Longest chain 26 peptides. Score 0.617 Round 5: 184 peptides, 15 chains. Longest chain 35 peptides. Score 0.625 Taking the results from Round 5 Chains 17, Residues 169, Estimated correctness of the model 24.2 % 1 chains (28 residues) have been docked in sequence ------------------------------------------------------ 5867 reflections ( 99.34 % complete ) and 3216 restraints for refining 1683 atoms. 2449 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2579 (Rfree = 0.000) for 1683 atoms. Found 10 (10 requested) and removed 13 (5 requested) atoms. Cycle 37: After refmac, R = 0.2503 (Rfree = 0.000) for 1666 atoms. Found 10 (10 requested) and removed 5 (5 requested) atoms. Cycle 38: After refmac, R = 0.2453 (Rfree = 0.000) for 1664 atoms. Found 10 (10 requested) and removed 8 (5 requested) atoms. Cycle 39: After refmac, R = 0.2339 (Rfree = 0.000) for 1664 atoms. Found 9 (10 requested) and removed 8 (5 requested) atoms. Cycle 40: After refmac, R = 0.2226 (Rfree = 0.000) for 1661 atoms. Found 4 (10 requested) and removed 6 (5 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.46 2.48 Search for helices and strands: 0 residues in 0 chains, 1742 seeds are put forward Round 1: 169 peptides, 17 chains. Longest chain 47 peptides. Score 0.557 Round 2: 175 peptides, 14 chains. Longest chain 46 peptides. Score 0.614 Round 3: 172 peptides, 14 chains. Longest chain 44 peptides. Score 0.606 Round 4: 177 peptides, 16 chains. Longest chain 37 peptides. Score 0.593 Round 5: 177 peptides, 15 chains. Longest chain 29 peptides. Score 0.606 Taking the results from Round 2 Chains 14, Residues 161, Estimated correctness of the model 20.0 % 1 chains (45 residues) have been docked in sequence ------------------------------------------------------ 5867 reflections ( 99.34 % complete ) and 3030 restraints for refining 1683 atoms. 2201 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2501 (Rfree = 0.000) for 1683 atoms. Found 10 (10 requested) and removed 16 (5 requested) atoms. Cycle 42: After refmac, R = 0.2324 (Rfree = 0.000) for 1669 atoms. Found 5 (10 requested) and removed 7 (5 requested) atoms. Cycle 43: After refmac, R = 0.2259 (Rfree = 0.000) for 1662 atoms. Found 7 (10 requested) and removed 7 (5 requested) atoms. Cycle 44: After refmac, R = 0.2243 (Rfree = 0.000) for 1659 atoms. Found 6 (10 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.2237 (Rfree = 0.000) for 1655 atoms. Found 4 (10 requested) and removed 7 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.52 2.53 Search for helices and strands: 0 residues in 0 chains, 1701 seeds are put forward Round 1: 180 peptides, 20 chains. Longest chain 26 peptides. Score 0.548 Round 2: 171 peptides, 16 chains. Longest chain 46 peptides. Score 0.577 Round 3: 182 peptides, 19 chains. Longest chain 28 peptides. Score 0.567 Round 4: 179 peptides, 14 chains. Longest chain 41 peptides. Score 0.625 Round 5: 181 peptides, 16 chains. Longest chain 25 peptides. Score 0.604 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 165, Estimated correctness of the model 24.2 % 1 chains (31 residues) have been docked in sequence Sequence coverage is 18 % Consider running further cycles of model building using 1zyb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 5867 reflections ( 99.34 % complete ) and 3258 restraints for refining 1683 atoms. 2487 conditional restraints added. Observations/parameters ratio is 0.87 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2704 (Rfree = 0.000) for 1683 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 47: After refmac, R = 0.2535 (Rfree = 0.000) for 1666 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 48: After refmac, R = 0.2476 (Rfree = 0.000) for 1654 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Cycle 49: After refmac, R = 0.2422 (Rfree = 0.000) for 1644 atoms. Found 0 (10 requested) and removed 5 (5 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:16:03 GMT 2018 Job finished. TimeTaking 48.13 Used memory is bytes: 11429928