null 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 1zyb-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zyb-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-3.2-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-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-3.2-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 22:23:12 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-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zyb-3.2-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 320 and 0 Target number of residues in the AU: 320 Target solvent content: 0.6272 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-3.2-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-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 1856 target number of atoms Had to go as low as 1.25 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 3.200 Wilson plot Bfac: 64.72 8256 reflections ( 99.53 % complete ) and 0 restraints for refining 2080 atoms. Observations/parameters ratio is 0.99 ------------------------------------------------------ Starting model: R = 0.3724 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3319 (Rfree = 0.000) for 2080 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.20 2.30 Search for helices and strands: 0 residues in 0 chains, 2126 seeds are put forward Round 1: 158 peptides, 18 chains. Longest chain 21 peptides. Score 0.510 Round 2: 176 peptides, 21 chains. Longest chain 20 peptides. Score 0.522 Round 3: 177 peptides, 19 chains. Longest chain 40 peptides. Score 0.553 Round 4: 175 peptides, 22 chains. Longest chain 26 peptides. Score 0.504 Round 5: 166 peptides, 21 chains. Longest chain 18 peptides. Score 0.491 Taking the results from Round 3 Chains 20, Residues 158, Estimated correctness of the model 27.8 % 1 chains (28 residues) have been docked in sequence ------------------------------------------------------ 8256 reflections ( 99.53 % complete ) and 3434 restraints for refining 1810 atoms. 2690 conditional restraints added. Observations/parameters ratio is 1.14 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3030 (Rfree = 0.000) for 1810 atoms. Found 16 (16 requested) and removed 13 (8 requested) atoms. Cycle 2: After refmac, R = 0.2872 (Rfree = 0.000) for 1791 atoms. Found 14 (16 requested) and removed 11 (8 requested) atoms. Cycle 3: After refmac, R = 0.2797 (Rfree = 0.000) for 1775 atoms. Found 13 (16 requested) and removed 8 (8 requested) atoms. Cycle 4: After refmac, R = 0.2731 (Rfree = 0.000) for 1765 atoms. Found 9 (15 requested) and removed 7 (7 requested) atoms. Cycle 5: After refmac, R = 0.2653 (Rfree = 0.000) for 1759 atoms. Found 7 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.18 2.28 Search for helices and strands: 0 residues in 0 chains, 1836 seeds are put forward Round 1: 178 peptides, 16 chains. Longest chain 29 peptides. Score 0.596 Round 2: 188 peptides, 14 chains. Longest chain 50 peptides. Score 0.647 Round 3: 189 peptides, 18 chains. Longest chain 23 peptides. Score 0.599 Round 4: 176 peptides, 15 chains. Longest chain 25 peptides. Score 0.604 Round 5: 187 peptides, 17 chains. Longest chain 22 peptides. Score 0.607 Taking the results from Round 2 Chains 15, Residues 174, Estimated correctness of the model 53.1 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 8256 reflections ( 99.53 % complete ) and 3099 restraints for refining 1695 atoms. 2295 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2900 (Rfree = 0.000) for 1695 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 7: After refmac, R = 0.2748 (Rfree = 0.000) for 1691 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 8: After refmac, R = 0.2645 (Rfree = 0.000) for 1683 atoms. Found 9 (15 requested) and removed 7 (7 requested) atoms. Cycle 9: After refmac, R = 0.2590 (Rfree = 0.000) for 1683 atoms. Found 4 (15 requested) and removed 11 (7 requested) atoms. Cycle 10: After refmac, R = 0.2572 (Rfree = 0.000) for 1675 atoms. Found 6 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.18 2.28 Search for helices and strands: 0 residues in 0 chains, 1729 seeds are put forward Round 1: 168 peptides, 18 chains. Longest chain 21 peptides. Score 0.540 Round 2: 182 peptides, 16 chains. Longest chain 22 peptides. Score 0.607 Round 3: 185 peptides, 14 chains. Longest chain 35 peptides. Score 0.640 Round 4: 191 peptides, 20 chains. Longest chain 34 peptides. Score 0.579 Round 5: 191 peptides, 15 chains. Longest chain 49 peptides. Score 0.642 Taking the results from Round 5 Chains 15, Residues 176, Estimated correctness of the model 51.9 % 2 chains (63 residues) have been docked in sequence ------------------------------------------------------ 8256 reflections ( 99.53 % complete ) and 3047 restraints for refining 1793 atoms. 2080 conditional restraints added. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3034 (Rfree = 0.000) for 1793 atoms. Found 16 (16 requested) and removed 27 (8 requested) atoms. Cycle 12: After refmac, R = 0.2889 (Rfree = 0.000) for 1766 atoms. Found 15 (15 requested) and removed 23 (7 requested) atoms. Cycle 13: After refmac, R = 0.2691 (Rfree = 0.000) for 1757 atoms. Found 15 (15 requested) and removed 18 (7 requested) atoms. Cycle 14: After refmac, R = 0.2767 (Rfree = 0.000) for 1750 atoms. Found 15 (15 requested) and removed 14 (7 requested) atoms. Cycle 15: After refmac, R = 0.2758 (Rfree = 0.000) for 1746 atoms. Found 15 (15 requested) and removed 17 (7 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.09 2.22 Search for helices and strands: 0 residues in 0 chains, 1805 seeds are put forward Round 1: 176 peptides, 16 chains. Longest chain 23 peptides. Score 0.590 Round 2: 189 peptides, 15 chains. Longest chain 42 peptides. Score 0.637 Round 3: 192 peptides, 17 chains. Longest chain 27 peptides. Score 0.620 Round 4: 187 peptides, 17 chains. Longest chain 36 peptides. Score 0.607 Round 5: 198 peptides, 13 chains. Longest chain 54 peptides. Score 0.682 Taking the results from Round 5 Chains 14, Residues 185, Estimated correctness of the model 61.3 % 3 chains (89 residues) have been docked in sequence ------------------------------------------------------ 8256 reflections ( 99.53 % complete ) and 2834 restraints for refining 1800 atoms. 1737 conditional restraints added. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2853 (Rfree = 0.000) for 1800 atoms. Found 16 (16 requested) and removed 20 (8 requested) atoms. Cycle 17: After refmac, R = 0.2790 (Rfree = 0.000) for 1785 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 18: After refmac, R = 0.2711 (Rfree = 0.000) for 1774 atoms. Found 16 (16 requested) and removed 15 (8 requested) atoms. Cycle 19: After refmac, R = 0.2712 (Rfree = 0.000) for 1768 atoms. Found 15 (15 requested) and removed 10 (7 requested) atoms. Cycle 20: After refmac, R = 0.2703 (Rfree = 0.000) for 1766 atoms. Found 15 (15 requested) and removed 8 (7 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.16 2.27 Search for helices and strands: 0 residues in 0 chains, 1821 seeds are put forward Round 1: 200 peptides, 11 chains. Longest chain 62 peptides. Score 0.709 Round 2: 191 peptides, 18 chains. Longest chain 28 peptides. Score 0.605 Round 3: 198 peptides, 16 chains. Longest chain 29 peptides. Score 0.647 Round 4: 200 peptides, 13 chains. Longest chain 40 peptides. Score 0.687 Round 5: 196 peptides, 15 chains. Longest chain 48 peptides. Score 0.654 Taking the results from Round 1 Chains 15, Residues 189, Estimated correctness of the model 67.1 % 3 chains (120 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 103 A 13 chains (190 residues) following loop building 2 chains (127 residues) in sequence following loop building ------------------------------------------------------ 8256 reflections ( 99.53 % complete ) and 2439 restraints for refining 1778 atoms. 1221 conditional restraints added. Observations/parameters ratio is 1.16 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2827 (Rfree = 0.000) for 1778 atoms. Found 15 (15 requested) and removed 31 (7 requested) atoms. Cycle 22: After refmac, R = 0.2567 (Rfree = 0.000) for 1756 atoms. Found 15 (15 requested) and removed 16 (7 requested) atoms. Cycle 23: After refmac, R = 0.2609 (Rfree = 0.000) for 1752 atoms. Found 14 (14 requested) and removed 18 (7 requested) atoms. Cycle 24: After refmac, R = 0.2571 (Rfree = 0.000) for 1743 atoms. Found 14 (14 requested) and removed 13 (7 requested) atoms. Cycle 25: After refmac, R = 0.2558 (Rfree = 0.000) for 1739 atoms. Found 14 (14 requested) and removed 14 (7 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.14 2.25 Search for helices and strands: 0 residues in 0 chains, 1808 seeds are put forward Round 1: 192 peptides, 13 chains. Longest chain 35 peptides. Score 0.668 Round 2: 200 peptides, 10 chains. Longest chain 60 peptides. Score 0.720 Round 3: 199 peptides, 14 chains. Longest chain 35 peptides. Score 0.673 Round 4: 198 peptides, 13 chains. Longest chain 47 peptides. Score 0.682 Round 5: 206 peptides, 13 chains. Longest chain 54 peptides. Score 0.700 Taking the results from Round 2 Chains 13, Residues 190, Estimated correctness of the model 69.3 % 4 chains (131 residues) have been docked in sequence Building loops using Loopy2018 13 chains (190 residues) following loop building 4 chains (131 residues) in sequence following loop building ------------------------------------------------------ 8256 reflections ( 99.53 % complete ) and 2665 restraints for refining 1841 atoms. 1386 conditional restraints added. Observations/parameters ratio is 1.12 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2629 (Rfree = 0.000) for 1841 atoms. Found 14 (14 requested) and removed 24 (8 requested) atoms. Cycle 27: After refmac, R = 0.2425 (Rfree = 0.000) for 1815 atoms. Found 14 (14 requested) and removed 14 (8 requested) atoms. Cycle 28: After refmac, R = 0.2391 (Rfree = 0.000) for 1810 atoms. Found 14 (14 requested) and removed 15 (8 requested) atoms. Cycle 29: After refmac, R = 0.2384 (Rfree = 0.000) for 1807 atoms. Found 13 (13 requested) and removed 11 (8 requested) atoms. Cycle 30: After refmac, R = 0.2328 (Rfree = 0.000) for 1805 atoms. Found 13 (13 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.13 2.25 Search for helices and strands: 0 residues in 0 chains, 1854 seeds are put forward Round 1: 203 peptides, 12 chains. Longest chain 62 peptides. Score 0.704 Round 2: 199 peptides, 15 chains. Longest chain 37 peptides. Score 0.661 Round 3: 198 peptides, 16 chains. Longest chain 34 peptides. Score 0.647 Round 4: 202 peptides, 16 chains. Longest chain 27 peptides. Score 0.657 Round 5: 202 peptides, 15 chains. Longest chain 43 peptides. Score 0.668 Taking the results from Round 1 Chains 14, Residues 191, Estimated correctness of the model 66.0 % 4 chains (128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 168 A and 176 A 12 chains (194 residues) following loop building 3 chains (135 residues) in sequence following loop building ------------------------------------------------------ 8256 reflections ( 99.53 % complete ) and 2589 restraints for refining 1835 atoms. 1264 conditional restraints added. Observations/parameters ratio is 1.12 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2633 (Rfree = 0.000) for 1835 atoms. Found 13 (13 requested) and removed 35 (8 requested) atoms. Cycle 32: After refmac, R = 0.2492 (Rfree = 0.000) for 1805 atoms. Found 12 (12 requested) and removed 16 (8 requested) atoms. Cycle 33: After refmac, R = 0.2416 (Rfree = 0.000) for 1799 atoms. Found 12 (12 requested) and removed 14 (8 requested) atoms. Cycle 34: After refmac, R = 0.2385 (Rfree = 0.000) for 1796 atoms. Found 12 (12 requested) and removed 9 (8 requested) atoms. Cycle 35: After refmac, R = 0.2346 (Rfree = 0.000) for 1795 atoms. Found 12 (12 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 2.26 Search for helices and strands: 0 residues in 0 chains, 1861 seeds are put forward Round 1: 207 peptides, 14 chains. Longest chain 34 peptides. Score 0.691 Round 2: 198 peptides, 12 chains. Longest chain 46 peptides. Score 0.693 Round 3: 201 peptides, 14 chains. Longest chain 47 peptides. Score 0.677 Round 4: 207 peptides, 10 chains. Longest chain 54 peptides. Score 0.734 Round 5: 200 peptides, 11 chains. Longest chain 45 peptides. Score 0.709 Taking the results from Round 4 Chains 10, Residues 197, Estimated correctness of the model 72.1 % 4 chains (148 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 167 A and 178 A 8 chains (202 residues) following loop building 3 chains (158 residues) in sequence following loop building ------------------------------------------------------ 8256 reflections ( 99.53 % complete ) and 2399 restraints for refining 1895 atoms. 937 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2648 (Rfree = 0.000) for 1895 atoms. Found 12 (12 requested) and removed 34 (8 requested) atoms. Cycle 37: After refmac, R = 0.2492 (Rfree = 0.000) for 1869 atoms. Found 11 (11 requested) and removed 25 (8 requested) atoms. Cycle 38: After refmac, R = 0.2378 (Rfree = 0.000) for 1848 atoms. Found 11 (11 requested) and removed 19 (8 requested) atoms. Cycle 39: After refmac, R = 0.2305 (Rfree = 0.000) for 1837 atoms. Found 10 (10 requested) and removed 18 (8 requested) atoms. Cycle 40: After refmac, R = 0.2283 (Rfree = 0.000) for 1827 atoms. Found 10 (10 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.09 2.22 Search for helices and strands: 0 residues in 0 chains, 1893 seeds are put forward Round 1: 193 peptides, 13 chains. Longest chain 44 peptides. Score 0.671 Round 2: 209 peptides, 13 chains. Longest chain 40 peptides. Score 0.706 Round 3: 207 peptides, 11 chains. Longest chain 56 peptides. Score 0.723 Round 4: 208 peptides, 13 chains. Longest chain 48 peptides. Score 0.704 Round 5: 204 peptides, 16 chains. Longest chain 33 peptides. Score 0.661 Taking the results from Round 3 Chains 12, Residues 196, Estimated correctness of the model 69.9 % 5 chains (154 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 87 A and 93 A Built loop between residues 165 A and 175 A Built loop between residues 205 A and 208 A 7 chains (206 residues) following loop building 2 chains (170 residues) in sequence following loop building ------------------------------------------------------ 8256 reflections ( 99.53 % complete ) and 2371 restraints for refining 1902 atoms. 849 conditional restraints added. Observations/parameters ratio is 1.09 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2783 (Rfree = 0.000) for 1902 atoms. Found 10 (10 requested) and removed 40 (8 requested) atoms. Cycle 42: After refmac, R = 0.2496 (Rfree = 0.000) for 1864 atoms. Found 9 (9 requested) and removed 23 (8 requested) atoms. Cycle 43: After refmac, R = 0.2361 (Rfree = 0.000) for 1843 atoms. Found 9 (9 requested) and removed 20 (8 requested) atoms. Cycle 44: After refmac, R = 0.2267 (Rfree = 0.000) for 1829 atoms. Found 9 (9 requested) and removed 23 (8 requested) atoms. Cycle 45: After refmac, R = 0.2186 (Rfree = 0.000) for 1814 atoms. Found 8 (8 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.22 Search for helices and strands: 0 residues in 0 chains, 1865 seeds are put forward Round 1: 209 peptides, 13 chains. Longest chain 44 peptides. Score 0.706 Round 2: 203 peptides, 12 chains. Longest chain 51 peptides. Score 0.704 Round 3: 201 peptides, 12 chains. Longest chain 45 peptides. Score 0.700 Round 4: 202 peptides, 13 chains. Longest chain 23 peptides. Score 0.691 Round 5: 209 peptides, 11 chains. Longest chain 42 peptides. Score 0.727 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 198, Estimated correctness of the model 70.7 % 4 chains (123 residues) have been docked in sequence Sequence coverage is 61 % Consider running further cycles of model building using 1zyb-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 50 A and 59 A Built loop between residues 78 A and 90 A 8 chains (207 residues) following loop building 2 chains (142 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8256 reflections ( 99.53 % complete ) and 2403 restraints for refining 1855 atoms. 977 conditional restraints added. Observations/parameters ratio is 1.11 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2670 (Rfree = 0.000) for 1855 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2516 (Rfree = 0.000) for 1827 atoms. Found 0 (8 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2401 (Rfree = 0.000) for 1809 atoms. Found 0 (8 requested) and removed 3 (8 requested) atoms. Cycle 49: After refmac, R = 0.2300 (Rfree = 0.000) for 1803 atoms. Found 0 (8 requested) and removed 2 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:13:45 GMT 2018 Job finished. TimeTaking 50.73 Used memory is bytes: 9381856