null Tue 25 Dec 19:27:57 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-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-3.4-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-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-3.4-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 19:28:06 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-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-3.4-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 309 and 0 Target number of residues in the AU: 309 Target solvent content: 0.6400 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-3.4-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-3.4-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 3.400 Wilson plot Bfac: 71.59 6914 reflections ( 99.44 % complete ) and 0 restraints for refining 2080 atoms. Observations/parameters ratio is 0.83 ------------------------------------------------------ Starting model: R = 0.3837 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3242 (Rfree = 0.000) for 2080 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.35 2.41 Search for helices and strands: 0 residues in 0 chains, 2127 seeds are put forward Round 1: 153 peptides, 21 chains. Longest chain 18 peptides. Score 0.448 Round 2: 183 peptides, 19 chains. Longest chain 27 peptides. Score 0.570 Round 3: 187 peptides, 19 chains. Longest chain 29 peptides. Score 0.581 Round 4: 189 peptides, 15 chains. Longest chain 38 peptides. Score 0.637 Round 5: 189 peptides, 16 chains. Longest chain 40 peptides. Score 0.625 Taking the results from Round 4 Chains 15, Residues 174, Estimated correctness of the model 40.3 % 1 chains (37 residues) have been docked in sequence ------------------------------------------------------ 6914 reflections ( 99.44 % complete ) and 3226 restraints for refining 1742 atoms. 2409 conditional restraints added. Observations/parameters ratio is 0.99 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2930 (Rfree = 0.000) for 1742 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 2: After refmac, R = 0.2679 (Rfree = 0.000) for 1714 atoms. Found 12 (13 requested) and removed 8 (6 requested) atoms. Cycle 3: After refmac, R = 0.2566 (Rfree = 0.000) for 1703 atoms. Found 9 (12 requested) and removed 9 (6 requested) atoms. Cycle 4: After refmac, R = 0.2510 (Rfree = 0.000) for 1688 atoms. Found 5 (12 requested) and removed 7 (6 requested) atoms. Cycle 5: After refmac, R = 0.2526 (Rfree = 0.000) for 1681 atoms. Found 4 (12 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 1776 seeds are put forward Round 1: 181 peptides, 18 chains. Longest chain 30 peptides. Score 0.578 Round 2: 190 peptides, 19 chains. Longest chain 26 peptides. Score 0.589 Round 3: 184 peptides, 18 chains. Longest chain 25 peptides. Score 0.586 Round 4: 191 peptides, 15 chains. Longest chain 35 peptides. Score 0.642 Round 5: 187 peptides, 15 chains. Longest chain 47 peptides. Score 0.632 Taking the results from Round 4 Chains 15, Residues 176, Estimated correctness of the model 41.8 % 2 chains (59 residues) have been docked in sequence ------------------------------------------------------ 6914 reflections ( 99.44 % complete ) and 3069 restraints for refining 1765 atoms. 2145 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2801 (Rfree = 0.000) for 1765 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 7: After refmac, R = 0.2542 (Rfree = 0.000) for 1743 atoms. Found 9 (13 requested) and removed 8 (6 requested) atoms. Cycle 8: After refmac, R = 0.2561 (Rfree = 0.000) for 1736 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 9: After refmac, R = 0.2395 (Rfree = 0.000) for 1729 atoms. Found 8 (13 requested) and removed 9 (6 requested) atoms. Cycle 10: After refmac, R = 0.2365 (Rfree = 0.000) for 1721 atoms. Found 9 (13 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.35 2.41 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward Round 1: 190 peptides, 14 chains. Longest chain 51 peptides. Score 0.652 Round 2: 184 peptides, 13 chains. Longest chain 33 peptides. Score 0.650 Round 3: 207 peptides, 15 chains. Longest chain 35 peptides. Score 0.680 Round 4: 184 peptides, 12 chains. Longest chain 34 peptides. Score 0.662 Round 5: 192 peptides, 15 chains. Longest chain 38 peptides. Score 0.645 Taking the results from Round 3 Chains 15, Residues 192, Estimated correctness of the model 52.6 % 3 chains (79 residues) have been docked in sequence ------------------------------------------------------ 6914 reflections ( 99.44 % complete ) and 2806 restraints for refining 1733 atoms. 1748 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2764 (Rfree = 0.000) for 1733 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 12: After refmac, R = 0.2561 (Rfree = 0.000) for 1717 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 13: After refmac, R = 0.2587 (Rfree = 0.000) for 1711 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 14: After refmac, R = 0.2380 (Rfree = 0.000) for 1705 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. Cycle 15: After refmac, R = 0.2317 (Rfree = 0.000) for 1698 atoms. Found 5 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.35 2.41 Search for helices and strands: 0 residues in 0 chains, 1752 seeds are put forward Round 1: 187 peptides, 16 chains. Longest chain 32 peptides. Score 0.620 Round 2: 193 peptides, 15 chains. Longest chain 46 peptides. Score 0.647 Round 3: 198 peptides, 15 chains. Longest chain 31 peptides. Score 0.659 Round 4: 200 peptides, 14 chains. Longest chain 47 peptides. Score 0.675 Round 5: 201 peptides, 15 chains. Longest chain 51 peptides. Score 0.666 Taking the results from Round 4 Chains 15, Residues 186, Estimated correctness of the model 51.2 % 4 chains (103 residues) have been docked in sequence ------------------------------------------------------ 6914 reflections ( 99.44 % complete ) and 2752 restraints for refining 1778 atoms. 1590 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2758 (Rfree = 0.000) for 1778 atoms. Found 13 (13 requested) and removed 26 (6 requested) atoms. Cycle 17: After refmac, R = 0.2486 (Rfree = 0.000) for 1760 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 18: After refmac, R = 0.2372 (Rfree = 0.000) for 1750 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 19: After refmac, R = 0.2273 (Rfree = 0.000) for 1742 atoms. Found 5 (13 requested) and removed 11 (6 requested) atoms. Cycle 20: After refmac, R = 0.2439 (Rfree = 0.000) for 1736 atoms. Found 13 (13 requested) and removed 6 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.33 2.39 Search for helices and strands: 0 residues in 0 chains, 1792 seeds are put forward Round 1: 195 peptides, 12 chains. Longest chain 45 peptides. Score 0.687 Round 2: 191 peptides, 16 chains. Longest chain 30 peptides. Score 0.630 Round 3: 188 peptides, 14 chains. Longest chain 23 peptides. Score 0.647 Round 4: 191 peptides, 15 chains. Longest chain 44 peptides. Score 0.642 Round 5: 190 peptides, 15 chains. Longest chain 46 peptides. Score 0.640 Taking the results from Round 1 Chains 16, Residues 183, Estimated correctness of the model 54.5 % 3 chains (74 residues) have been docked in sequence ------------------------------------------------------ 6914 reflections ( 99.44 % complete ) and 2802 restraints for refining 1694 atoms. 1784 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2556 (Rfree = 0.000) for 1694 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 22: After refmac, R = 0.2392 (Rfree = 0.000) for 1682 atoms. Found 12 (12 requested) and removed 8 (6 requested) atoms. Cycle 23: After refmac, R = 0.2272 (Rfree = 0.000) for 1678 atoms. Found 11 (12 requested) and removed 9 (6 requested) atoms. Cycle 24: After refmac, R = 0.2224 (Rfree = 0.000) for 1678 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 25: After refmac, R = 0.2201 (Rfree = 0.000) for 1674 atoms. Found 3 (12 requested) and removed 7 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.34 2.40 Search for helices and strands: 0 residues in 0 chains, 1716 seeds are put forward Round 1: 193 peptides, 15 chains. Longest chain 27 peptides. Score 0.647 Round 2: 196 peptides, 15 chains. Longest chain 36 peptides. Score 0.654 Round 3: 191 peptides, 14 chains. Longest chain 35 peptides. Score 0.654 Round 4: 198 peptides, 14 chains. Longest chain 44 peptides. Score 0.671 Round 5: 202 peptides, 13 chains. Longest chain 58 peptides. Score 0.691 Taking the results from Round 5 Chains 17, Residues 189, Estimated correctness of the model 55.5 % 4 chains (107 residues) have been docked in sequence ------------------------------------------------------ 6914 reflections ( 99.44 % complete ) and 2700 restraints for refining 1800 atoms. 1509 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2998 (Rfree = 0.000) for 1800 atoms. Found 13 (13 requested) and removed 30 (6 requested) atoms. Cycle 27: After refmac, R = 0.2780 (Rfree = 0.000) for 1769 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 28: After refmac, R = 0.2785 (Rfree = 0.000) for 1757 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 29: After refmac, R = 0.2794 (Rfree = 0.000) for 1740 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 30: After refmac, R = 0.2651 (Rfree = 0.000) for 1735 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.30 2.37 Search for helices and strands: 0 residues in 0 chains, 1794 seeds are put forward Round 1: 180 peptides, 17 chains. Longest chain 26 peptides. Score 0.588 Round 2: 190 peptides, 15 chains. Longest chain 36 peptides. Score 0.640 Round 3: 185 peptides, 16 chains. Longest chain 25 peptides. Score 0.614 Round 4: 178 peptides, 15 chains. Longest chain 28 peptides. Score 0.609 Round 5: 189 peptides, 11 chains. Longest chain 37 peptides. Score 0.685 Taking the results from Round 5 Chains 12, Residues 178, Estimated correctness of the model 53.9 % 4 chains (101 residues) have been docked in sequence ------------------------------------------------------ 6914 reflections ( 99.44 % complete ) and 2721 restraints for refining 1787 atoms. 1565 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2875 (Rfree = 0.000) for 1787 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 32: After refmac, R = 0.2621 (Rfree = 0.000) for 1773 atoms. Found 10 (13 requested) and removed 12 (6 requested) atoms. Cycle 33: After refmac, R = 0.2690 (Rfree = 0.000) for 1760 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 34: After refmac, R = 0.2611 (Rfree = 0.000) for 1750 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 35: After refmac, R = 0.2540 (Rfree = 0.000) for 1742 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.35 2.41 Search for helices and strands: 0 residues in 0 chains, 1807 seeds are put forward Round 1: 183 peptides, 17 chains. Longest chain 26 peptides. Score 0.596 Round 2: 186 peptides, 14 chains. Longest chain 28 peptides. Score 0.642 Round 3: 188 peptides, 15 chains. Longest chain 36 peptides. Score 0.635 Round 4: 199 peptides, 15 chains. Longest chain 43 peptides. Score 0.661 Round 5: 182 peptides, 13 chains. Longest chain 28 peptides. Score 0.645 Taking the results from Round 4 Chains 17, Residues 184, Estimated correctness of the model 47.3 % 3 chains (68 residues) have been docked in sequence ------------------------------------------------------ 6914 reflections ( 99.44 % complete ) and 2903 restraints for refining 1721 atoms. 1890 conditional restraints added. Observations/parameters ratio is 1.00 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2911 (Rfree = 0.000) for 1721 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 37: After refmac, R = 0.2697 (Rfree = 0.000) for 1713 atoms. Found 12 (12 requested) and removed 18 (6 requested) atoms. Cycle 38: After refmac, R = 0.2702 (Rfree = 0.000) for 1696 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 39: After refmac, R = 0.2433 (Rfree = 0.000) for 1696 atoms. Found 4 (12 requested) and removed 8 (6 requested) atoms. Cycle 40: After refmac, R = 0.2367 (Rfree = 0.000) for 1691 atoms. Found 2 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.37 2.42 Search for helices and strands: 0 residues in 0 chains, 1738 seeds are put forward Round 1: 182 peptides, 19 chains. Longest chain 24 peptides. Score 0.567 Round 2: 196 peptides, 15 chains. Longest chain 31 peptides. Score 0.654 Round 3: 203 peptides, 15 chains. Longest chain 39 peptides. Score 0.671 Round 4: 203 peptides, 12 chains. Longest chain 60 peptides. Score 0.704 Round 5: 191 peptides, 14 chains. Longest chain 35 peptides. Score 0.654 Taking the results from Round 4 Chains 15, Residues 191, Estimated correctness of the model 58.9 % 3 chains (95 residues) have been docked in sequence Building loops using Loopy2018 15 chains (191 residues) following loop building 3 chains (95 residues) in sequence following loop building ------------------------------------------------------ 6914 reflections ( 99.44 % complete ) and 2701 restraints for refining 1755 atoms. 1546 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2975 (Rfree = 0.000) for 1755 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 42: After refmac, R = 0.2756 (Rfree = 0.000) for 1746 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 43: After refmac, R = 0.2614 (Rfree = 0.000) for 1743 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 44: After refmac, R = 0.2724 (Rfree = 0.000) for 1740 atoms. Found 12 (12 requested) and removed 17 (6 requested) atoms. Cycle 45: After refmac, R = 0.2649 (Rfree = 0.000) for 1731 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.31 2.38 Search for helices and strands: 0 residues in 0 chains, 1763 seeds are put forward Round 1: 175 peptides, 16 chains. Longest chain 36 peptides. Score 0.588 Round 2: 190 peptides, 16 chains. Longest chain 44 peptides. Score 0.627 Round 3: 195 peptides, 15 chains. Longest chain 42 peptides. Score 0.652 Round 4: 187 peptides, 15 chains. Longest chain 30 peptides. Score 0.632 Round 5: 181 peptides, 14 chains. Longest chain 46 peptides. Score 0.630 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 180, Estimated correctness of the model 44.7 % 2 chains (59 residues) have been docked in sequence Sequence coverage is 32 % Consider running further cycles of model building using 1zyb-3_warpNtrace.pdb as input Building loops using Loopy2018 15 chains (180 residues) following loop building 2 chains (59 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6914 reflections ( 99.44 % complete ) and 2962 restraints for refining 1711 atoms. 2013 conditional restraints added. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2958 (Rfree = 0.000) for 1711 atoms. Found 0 (11 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2923 (Rfree = 0.000) for 1701 atoms. Found 0 (11 requested) and removed 3 (6 requested) atoms. Cycle 48: After refmac, R = 0.2773 (Rfree = 0.000) for 1698 atoms. Found 0 (11 requested) and removed 0 (6 requested) atoms. Cycle 49: After refmac, R = 0.2701 (Rfree = 0.000) for 1696 atoms. Found 0 (11 requested) and removed 1 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:18:13 GMT 2018 Job finished. TimeTaking 50.27 Used memory is bytes: 2869064